diff --git a/taverna-commandline-1.2/pom.xml b/taverna-commandline-1.2/pom.xml
deleted file mode 100644
index f19408b..0000000
--- a/taverna-commandline-1.2/pom.xml
+++ /dev/null
@@ -1,117 +0,0 @@
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
-	<modelVersion>4.0.0</modelVersion>
-	<parent>
-		<artifactId>parent</artifactId>
-		<groupId>net.sf.taverna</groupId>
-		<version>0.1.2009-02-12</version>
-	</parent>
-	<groupId>net.sf.taverna.t2.taverna-commandline</groupId>
-	<artifactId>taverna-commandline</artifactId>
-	<version>1.2</version>
-	<packaging>pom</packaging>	
-	
-	<properties>
-		<t2.core.version>1.2</t2.core.version>
-		<t2.reference-core-extensions.version>1.2</t2.reference-core-extensions.version>
-		<t2.infrastructure.version>2.2</t2.infrastructure.version>
-		<t2.core.provenanceconnector.version>1.2</t2.core.provenanceconnector.version>
-		<taverna.version>1.7.2.2</taverna.version>
-		<t2.ui-components.version>1.2</t2.ui-components.version>
-	</properties>
-
-	<name>Taverna Commandline</name>
-	<scm>
-		<connection>scm:svn:http://taverna.googlecode.com/svn/taverna/engine/net.sf.taverna.t2.taverna-commandline/tags/taverna-commandline-1.2/</connection>
-		<developerConnection>scm:svn:https://taverna.googlecode.com/svn/taverna/engine/net.sf.taverna.t2.taverna-commandline/tags/taverna-commandline-1.2/</developerConnection>
-		<url>http://code.google.com/p/taverna/source/browse/#svn/taverna/engine/net.sf.taverna.t2.taverna-commandline/tags/taverna-commandline-1.2/</url>
-	</scm>
-	<build>
-		<plugins>
-			<plugin>
-				<artifactId>maven-clover-plugin</artifactId>
-				<executions>
-					<execution>
-						<phase>pre-site</phase>
-						<goals>
-							<goal>instrument</goal>
-							<goal>aggregate</goal>
-						</goals>
-					</execution>
-				</executions>
-				<configuration>
-					<jdk>1.5</jdk>
-					<targetPercentage>50%</targetPercentage>
-					<failOnViolation>false</failOnViolation>
-				</configuration>
-			</plugin>
-		</plugins>
-	</build>
-
-	<modules>
-		<module>taverna-commandline-common</module>
-	</modules>
-
-	<repositories>
-		<repository>
-			<releases />
-			<snapshots>
-				<enabled>false</enabled>
-			</snapshots>
-			<id>mygrid-repository</id>
-			<name>myGrid Repository</name>
-			<url>http://www.mygrid.org.uk/maven/repository</url>
-		</repository>
-	</repositories>
-	<reporting>
-		<plugins>
-			<plugin>
-				<artifactId>maven-checkstyle-plugin</artifactId>
-				<configuration>
-					<configLocation>
-						${basedir}/../checkstyle.xml
-					</configLocation>
-				</configuration>
-			</plugin>
-			<plugin>
-				<artifactId>maven-clover-plugin</artifactId>
-				<configuration>
-					<generatePdf>true</generatePdf>
-					<generateXml>true</generateXml>
-				</configuration>
-			</plugin>
-			<plugin>
-				<artifactId>maven-javadoc-plugin</artifactId>
-				<configuration>
-					<minmemory>128m</minmemory>
-					<maxmemory>512</maxmemory>
-					<aggregate>true</aggregate>
-					<links>
-						<link>
-							http://www.mygrid.org.uk/taverna/api/
-						</link>
-						<link>
-							http://java.sun.com/j2se/1.5.0/docs/api/
-						</link>
-					</links>
-				</configuration>
-			</plugin>
-			<plugin>
-				<artifactId>maven-surefire-plugin</artifactId>
-				<configuration>
-					<systemProperties>
-						<property>
-							<name>java.awt.headless</name>
-							<value>true</value>
-						</property>
-					</systemProperties>
-				</configuration>
-			</plugin>
-			<plugin>
-				<groupId>org.codehaus.mojo</groupId>
-				<artifactId>jxr-maven-plugin</artifactId>
-			</plugin>
-		</plugins>
-	</reporting>
-
-</project>
diff --git a/taverna-commandline-1.2/taverna-commandline-common/pom.xml b/taverna-commandline-1.2/taverna-commandline-common/pom.xml
deleted file mode 100644
index 8512535..0000000
--- a/taverna-commandline-1.2/taverna-commandline-common/pom.xml
+++ /dev/null
@@ -1,87 +0,0 @@
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
-	<modelVersion>4.0.0</modelVersion>
-	<parent>
-		<groupId>net.sf.taverna.t2.taverna-commandline</groupId>
-		<artifactId>taverna-commandline</artifactId>
-		<version>1.2</version>
-	</parent>
-	<groupId>net.sf.taverna.t2.taverna-commandline</groupId>
-	<artifactId>taverna-commandline-common</artifactId>
-	<packaging>jar</packaging>
-
-
-	<name>Taverna Commandline Common</name>
-	<dependencies>
-
-		<dependency>
-			<groupId>net.sf.taverna.t2.infrastructure</groupId>
-			<artifactId>launcher-api</artifactId>
-			<version>${t2.infrastructure.version}</version>
-		</dependency>
-
-		<dependency>
-			<groupId>net.sf.taverna.t2.core</groupId>
-			<artifactId>workflowmodel-api</artifactId>
-			<version>${t2.core.version}</version>
-		</dependency>
-
-		<dependency>
-			<groupId>uk.org.mygrid.taverna.baclava</groupId>
-			<artifactId>baclava-core</artifactId>
-			<version>${taverna.version}</version>
-		</dependency>
-
-		<dependency>
-			<groupId>net.sf.taverna.t2.ui-impl</groupId>
-			<artifactId>data-management-config</artifactId>
-			<version>${t2.core.version}</version>
-		</dependency>
-
-		<dependency>
-			<groupId>net.sf.taverna.t2.core</groupId>
-			<artifactId>reference-impl</artifactId>
-			<version>${t2.core.version}</version>
-		</dependency>
-
-		<dependency>
-			<groupId>net.sf.taverna.t2.core</groupId>
-			<artifactId>provenanceconnector</artifactId>
-			<version>${t2.core.provenanceconnector.version}</version>
-		</dependency>
-
-		<dependency>
-			<groupId>net.sf.taverna.t2.core</groupId>
-			<artifactId>reference-core-extensions</artifactId>
-			<version>${t2.reference-core-extensions.version}</version>
-		</dependency>
-
-		<dependency>
-			<groupId>commons-cli</groupId>
-			<artifactId>commons-cli</artifactId>
-			<version>1.2</version>
-		</dependency>
-
-		<dependency>
-			<groupId>commons-io</groupId>
-			<artifactId>commons-io</artifactId>
-			<version>1.4</version>
-		</dependency>
-		
-		<dependency>
-			<groupId>uk.org.mygrid.resources.mimeutil</groupId>
-			<artifactId>mime-util</artifactId>
-			<version>2.1.2-3</version>
-		</dependency>
-
-		<!--  TEST -->
-		<dependency>
-			<groupId>junit</groupId>
-			<artifactId>junit</artifactId>
-			<version>4.4</version>
-			<scope>test</scope>
-		</dependency>
-		
-	</dependencies>
-
-</project>
diff --git a/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/CommandLineInvocationContext.java b/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/CommandLineInvocationContext.java
deleted file mode 100644
index 5c60ddf..0000000
--- a/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/CommandLineInvocationContext.java
+++ /dev/null
@@ -1,78 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester   
- * 
- *  Modifications to the initial code base are copyright of their
- *  respective authors, or their employers as appropriate.
- * 
- *  This program is free software; you can redistribute it and/or
- *  modify it under the terms of the GNU Lesser General Public License
- *  as published by the Free Software Foundation; either version 2.1 of
- *  the License, or (at your option) any later version.
- *    
- *  This program is distributed in the hope that it will be useful, but
- *  WITHOUT ANY WARRANTY; without even the implied warranty of
- *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
- *  Lesser General Public License for more details.
- *    
- *  You should have received a copy of the GNU Lesser General Public
- *  License along with this program; if not, write to the Free Software
- *  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.commandline;
-
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.List;
-
-import net.sf.taverna.t2.invocation.InvocationContext;
-import net.sf.taverna.t2.provenance.reporter.ProvenanceReporter;
-import net.sf.taverna.t2.reference.ReferenceService;
-/**
- * An InvocationContext used by the command line tool.
- * 
- * @author Stuart Owen
- *
- */
-public class CommandLineInvocationContext implements InvocationContext {
-
-	private final ReferenceService referenceService;
-
-	private final ProvenanceReporter provenanceReporter;
-
-	private List<Object> entities = Collections
-			.synchronizedList(new ArrayList<Object>());
-
-	public CommandLineInvocationContext(ReferenceService referenceService,
-			ProvenanceReporter provenanceReporter) {
-		this.referenceService = referenceService;
-		this.provenanceReporter = provenanceReporter;
-	}
-
-	public void addEntity(Object entity) {
-		entities.add(entity);
-	}
-
-	public <T extends Object> List<T> getEntities(Class<T> entityType) {
-		List<T> entitiesOfType = new ArrayList<T>();
-		synchronized (entities) {
-			for (Object entity : entities) {
-				if (entityType.isInstance(entity)) {
-					entitiesOfType.add(entityType.cast(entity));
-				}
-			}
-		}
-		return entitiesOfType;
-	}
-
-	public ProvenanceReporter getProvenanceReporter() {
-		return provenanceReporter;
-	}
-
-	public ReferenceService getReferenceService() {
-		return referenceService;
-	}
-
-	public void removeEntity(Object entity) {
-		entities.remove(entity);
-	}
-}
\ No newline at end of file
diff --git a/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/CommandLineLauncher.java b/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/CommandLineLauncher.java
deleted file mode 100644
index f3274b5..0000000
--- a/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/CommandLineLauncher.java
+++ /dev/null
@@ -1,415 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester   
- * 
- *  Modifications to the initial code base are copyright of their
- *  respective authors, or their employers as appropriate.
- * 
- *  This program is free software; you can redistribute it and/or
- *  modify it under the terms of the GNU Lesser General Public License
- *  as published by the Free Software Foundation; either version 2.1 of
- *  the License, or (at your option) any later version.
- *    
- *  This program is distributed in the hope that it will be useful, but
- *  WITHOUT ANY WARRANTY; without even the implied warranty of
- *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
- *  Lesser General Public License for more details.
- *    
- *  You should have received a copy of the GNU Lesser General Public
- *  License along with this program; if not, write to the Free Software
- *  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.commandline;
-
-import java.io.File;
-import java.io.IOException;
-import java.io.InputStream;
-import java.net.MalformedURLException;
-import java.net.URISyntaxException;
-import java.net.URL;
-import java.sql.SQLException;
-import java.util.HashMap;
-import java.util.Map;
-
-import javax.naming.NamingException;
-
-import net.sf.taverna.platform.spring.RavenAwareClassPathXmlApplicationContext;
-import net.sf.taverna.raven.launcher.Launchable;
-import net.sf.taverna.t2.commandline.data.DatabaseConfigurationHandler;
-import net.sf.taverna.t2.commandline.data.InputsHandler;
-import net.sf.taverna.t2.commandline.data.SaveResultsHandler;
-import net.sf.taverna.t2.commandline.exceptions.DatabaseConfigurationException;
-import net.sf.taverna.t2.commandline.exceptions.InvalidOptionException;
-import net.sf.taverna.t2.commandline.exceptions.OpenDataflowException;
-import net.sf.taverna.t2.commandline.exceptions.ReadInputException;
-import net.sf.taverna.t2.commandline.options.CommandLineOptions;
-import net.sf.taverna.t2.facade.WorkflowInstanceFacade;
-import net.sf.taverna.t2.invocation.InvocationContext;
-import net.sf.taverna.t2.invocation.TokenOrderException;
-import net.sf.taverna.t2.invocation.WorkflowDataToken;
-import net.sf.taverna.t2.provenance.ProvenanceConnectorFactory;
-import net.sf.taverna.t2.provenance.ProvenanceConnectorFactoryRegistry;
-import net.sf.taverna.t2.provenance.connector.ProvenanceConnector;
-import net.sf.taverna.t2.reference.ReferenceService;
-import net.sf.taverna.t2.workbench.reference.config.DataManagementConfiguration;
-import net.sf.taverna.t2.workflowmodel.Dataflow;
-import net.sf.taverna.t2.workflowmodel.DataflowInputPort;
-import net.sf.taverna.t2.workflowmodel.DataflowOutputPort;
-import net.sf.taverna.t2.workflowmodel.DataflowValidationReport;
-import net.sf.taverna.t2.workflowmodel.EditException;
-import net.sf.taverna.t2.workflowmodel.Edits;
-import net.sf.taverna.t2.workflowmodel.EditsRegistry;
-import net.sf.taverna.t2.workflowmodel.InvalidDataflowException;
-import net.sf.taverna.t2.workflowmodel.serialization.DeserializationException;
-import net.sf.taverna.t2.workflowmodel.serialization.xml.XMLDeserializer;
-import net.sf.taverna.t2.workflowmodel.serialization.xml.XMLDeserializerRegistry;
-
-import org.apache.log4j.Level;
-import org.apache.log4j.LogManager;
-import org.apache.log4j.Logger;
-import org.apache.log4j.PatternLayout;
-import org.apache.log4j.PropertyConfigurator;
-import org.apache.log4j.RollingFileAppender;
-import org.jdom.Element;
-import org.jdom.JDOMException;
-import org.jdom.input.SAXBuilder;
-import org.springframework.context.ApplicationContext;
-
-/**
- * A utility class that wraps the process of executing a workflow, allowing
- * workflows to be easily executed independently of the GUI.
- * 
- * @author Stuart Owen
- */
-
-public class CommandLineLauncher implements Launchable {
-
-	private static Logger logger = Logger.getLogger(CommandLineLauncher.class);
-
-	/**
-	 * Main method, purely for development and debugging purposes. Full
-	 * execution of workflows will not work through this method.
-	 * 
-	 * @param args
-	 * @throws Exception
-	 */
-	public static void main(String[] args) {
-		new CommandLineLauncher().launch(args);
-	}
-
-	public int launch(String[] args) {
-		
-		try {
-			CommandLineOptions options = new CommandLineOptions(args);
-			initialiseLogging(options);
-			return setupAndExecute(args,options);
-		} catch (EditException e) {
-			error("There was an error opening the workflow: " + e.getMessage());
-		} catch (DeserializationException e) {
-			error("There was an error opening the workflow: " + e.getMessage());
-		} catch (InvalidDataflowException e) {
-			error("There was an error validating the workflow: "
-					+ e.getMessage());
-		} catch (TokenOrderException e) {
-			error("There was an error starting the workflow execution: "
-					+ e.getMessage());
-		} catch (InvalidOptionException e) {
-			error(e.getMessage());
-		} catch (ReadInputException e) {
-			error(e.getMessage());
-		} catch (OpenDataflowException e) {
-			error(e.getMessage());
-		} catch (DatabaseConfigurationException e) {
-			error(e.getMessage());
-		}
-		return 0;
-	}
-
-	private void initialiseLogging(CommandLineOptions options) {
-		LogManager.resetConfiguration();
-
-		if (System.getProperty("log4j.configuration") == null) {
-			try {
-				PropertyConfigurator.configure(CommandLineLauncher.class
-						.getClassLoader().getResource("cl-log4j.properties")
-						.toURI().toURL());
-			} catch (MalformedURLException e) {
-				logger
-						.error(
-								"There was a serious error reading the default logging configuration",
-								e);
-			} catch (URISyntaxException e) {
-				logger
-						.error(
-								"There was a serious error reading the default logging configuration",
-								e);
-			}
-						
-		} else {			
-			PropertyConfigurator.configure(System
-					.getProperty("log4j.configuration"));
-		}	
-		
-		if (options.hasLogFile()) {
-			RollingFileAppender appender;
-			try {
-
-				PatternLayout layout = new PatternLayout(
-						"%-5p %d{ISO8601} (%c:%L) - %m%n");
-				appender = new RollingFileAppender(layout, options.getLogFile());
-				appender.setMaxFileSize("1MB");
-				appender.setEncoding("UTF-8");
-				appender.setMaxBackupIndex(4);
-				// Let root logger decide level
-				appender.setThreshold(Level.ALL);
-				LogManager.getRootLogger().addAppender(appender);
-			} catch (IOException e) {
-				System.err.println("Could not log to " + options.getLogFile());
-			}
-		}
-	}
-
-	public int setupAndExecute(String[] args,CommandLineOptions options) throws InvalidOptionException,
-			EditException, DeserializationException, InvalidDataflowException,
-			TokenOrderException, ReadInputException, OpenDataflowException,
-			DatabaseConfigurationException {
-
-		
-		if (!options.askedForHelp()) {
-			setupDatabase(options);
-
-			if (options.getWorkflow() != null) {
-				URL workflowURL = readWorkflowURL(options.getWorkflow());
-
-				Dataflow dataflow = openDataflow(workflowURL);
-				validateDataflow(dataflow);
-
-				InvocationContext context = createInvocationContext();
-
-				WorkflowInstanceFacade facade = compileFacade(dataflow, context);
-				InputsHandler inputsHandler = new InputsHandler();
-				Map<String, DataflowInputPort> portMap = new HashMap<String, DataflowInputPort>();
-
-				for (DataflowInputPort port : dataflow.getInputPorts()) {
-					portMap.put(port.getName(), port);
-				}
-				inputsHandler.checkProvidedInputs(portMap, options);
-				Map<String, WorkflowDataToken> inputs = inputsHandler
-						.registerInputs(portMap, options, context);
-
-				CommandLineResultListener resultListener = addResultListener(
-						facade, context, dataflow, options);
-
-				executeWorkflow(facade, inputs, resultListener);
-			}
-		} else {
-			options.displayHelp();
-		}
-
-		// wait until user hits CTRL-C before exiting
-		if (options.getStartDatabaseOnly()) {
-			// FIXME: need to do this more gracefully.
-			while (true) {
-				try {
-					Thread.sleep(500);
-				} catch (InterruptedException e) {
-					return 0;
-				}
-			}
-		}
-
-		return 0;
-	}
-
-	protected void validateDataflow(Dataflow dataflow)
-			throws InvalidDataflowException {
-		// FIXME: this needs expanding upon to give more details info back to
-		// the user
-		// FIXME: added a getMessage to InvalidDataflowException may be good
-		// place to do this.
-		DataflowValidationReport report = dataflow.checkValidity();
-		if (!report.isValid()) {
-			throw new InvalidDataflowException(dataflow, report);
-		}
-	}
-
-	protected void executeWorkflow(WorkflowInstanceFacade facade,
-			Map<String, WorkflowDataToken> inputs,
-			CommandLineResultListener resultListener)
-			throws TokenOrderException {
-		facade.fire();
-		for (String inputName : inputs.keySet()) {
-			WorkflowDataToken token = inputs.get(inputName);
-			facade.pushData(token, inputName);
-		}
-
-		while (!resultListener.isComplete()) {
-			try {
-				Thread.sleep(100);
-			} catch (InterruptedException e) {
-				logger
-						.warn(
-								"Thread Interuption Exception whilst waiting for dataflow completion",
-								e);
-			}
-		}
-	}
-
-	private void setupDatabase(CommandLineOptions options)
-			throws DatabaseConfigurationException {
-		DatabaseConfigurationHandler dbHandler = new DatabaseConfigurationHandler(
-				options);
-		dbHandler.configureDatabase();
-		if (!options.isInMemory()) {
-			try {
-				dbHandler.testDatabaseConnection();
-			} catch (NamingException e) {
-				throw new DatabaseConfigurationException(
-						"There was an error trying to setup the database datasource: "
-								+ e.getMessage(), e);
-			} catch (SQLException e) {
-				if (options.isClientServer()) {
-					throw new DatabaseConfigurationException(
-							"There was an error whilst making a test database connection. If running with -clientserver you should check that a server is running (check -startdb or -dbproperties)",
-							e);
-				}
-				if (options.isEmbedded()) {
-					throw new DatabaseConfigurationException(
-							"There was an error whilst making a test database connection. If running with -embedded you should make sure that another process isn't using the database, or a server running through -startdb",
-							e);
-				}
-			}
-		}
-
-	}
-
-	private InvocationContext createInvocationContext() {
-		ReferenceService referenceService = createReferenceServiceBean();
-		ProvenanceConnector connector = null;
-		DataManagementConfiguration dbConfig = DataManagementConfiguration
-				.getInstance();
-		if (dbConfig.isProvenanceEnabled()) {
-			String connectorType = dbConfig.getConnectorType();
-
-			for (ProvenanceConnectorFactory factory : ProvenanceConnectorFactoryRegistry
-					.getInstance().getInstances()) {
-				if (connectorType.equalsIgnoreCase(factory.getConnectorType())) {
-					connector = factory.getProvenanceConnector();
-				}
-
-			}
-			if (connector != null) {
-				connector.init();
-			} else {
-				error("Unable to initialise the provenance - the ProvenanceConnector cannot be found.");
-			}
-		}
-		InvocationContext context = new CommandLineInvocationContext(
-				referenceService, connector);
-		return context;
-	}
-
-	private File determineOutputDir(CommandLineOptions options,
-			String dataflowName) {
-		File result = null;
-		if (options.getOutputDirectory() != null) {
-			result = new File(options.getOutputDirectory());
-			if (result.exists()) {
-				error("The specified output directory '"
-						+ options.getOutputDirectory() + "' already exists");
-			}
-		} else if (options.getOutputDocument() == null) {
-			result = new File(dataflowName + "_output");
-			int x = 1;
-			while (result.exists()) {
-				result = new File(dataflowName + "_output_" + x);
-				x++;
-			}
-		}
-		if (result != null) {
-			System.out.println("Outputs will be saved to the directory: "
-					+ result.getAbsolutePath());
-		}
-		return result;
-	}
-
-	protected void error(String msg) {
-		System.err.println(msg);
-		System.exit(-1);
-	}
-
-	private URL readWorkflowURL(String workflowOption)
-			throws OpenDataflowException {
-		URL url;
-		try {
-			url = new URL("file:");
-			return new URL(url, workflowOption);
-		} catch (MalformedURLException e) {
-			throw new OpenDataflowException(
-					"The was an error processing the URL to the workflow: "
-							+ e.getMessage(), e);
-		}
-	}
-
-	private CommandLineResultListener addResultListener(
-			WorkflowInstanceFacade facade, InvocationContext context,
-			Dataflow dataflow, CommandLineOptions options) {
-		File outputDir = null;
-		File baclavaDoc = null;
-
-		if (options.saveResultsToDirectory()) {
-			outputDir = determineOutputDir(options, dataflow.getLocalName());
-		}
-		if (options.getOutputDocument() != null) {
-			baclavaDoc = new File(options.getOutputDocument());
-		}
-
-		Map<String, Integer> outputPortNamesAndDepth = new HashMap<String, Integer>();
-		for (DataflowOutputPort port : dataflow.getOutputPorts()) {
-			outputPortNamesAndDepth.put(port.getName(), port.getDepth());
-		}
-		SaveResultsHandler resultsHandler = new SaveResultsHandler(
-				outputPortNamesAndDepth, outputDir, baclavaDoc);
-		CommandLineResultListener listener = new CommandLineResultListener(
-				outputPortNamesAndDepth.size(), resultsHandler,
-				outputDir != null, baclavaDoc != null);
-		facade.addResultListener(listener);
-		return listener;
-
-	}
-
-	protected ReferenceService createReferenceServiceBean() {
-		ApplicationContext appContext = new RavenAwareClassPathXmlApplicationContext(
-				DataManagementConfiguration.getInstance().getDatabaseContext());
-		return (ReferenceService) appContext
-				.getBean("t2reference.service.referenceService");
-	}
-
-	protected WorkflowInstanceFacade compileFacade(Dataflow dataflow,
-			InvocationContext context) throws InvalidDataflowException {
-		Edits edits = EditsRegistry.getEdits();
-		return edits.createWorkflowInstanceFacade(dataflow, context, "");
-	}
-
-	protected Dataflow openDataflow(URL workflowURL)
-			throws DeserializationException, EditException,
-			OpenDataflowException {
-		XMLDeserializer deserializer = XMLDeserializerRegistry.getInstance()
-				.getDeserializer();
-		SAXBuilder builder = new SAXBuilder();
-		Element el;
-		try {
-			InputStream stream = workflowURL.openStream();
-			el = builder.build(stream).detachRootElement();
-		} catch (JDOMException e) {
-			throw new OpenDataflowException(
-					"There was a problem processing the workflow XML: "
-							+ e.getMessage(), e);
-		} catch (IOException e) {
-			throw new OpenDataflowException(
-					"There was a problem reading the workflow file: "
-							+ e.getMessage(), e);
-		}
-		return deserializer.deserializeDataflow(el);
-	}
-
-}
diff --git a/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/CommandLineResultListener.java b/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/CommandLineResultListener.java
deleted file mode 100644
index 3d72d0f..0000000
--- a/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/CommandLineResultListener.java
+++ /dev/null
@@ -1,81 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester   
- * 
- *  Modifications to the initial code base are copyright of their
- *  respective authors, or their employers as appropriate.
- * 
- *  This program is free software; you can redistribute it and/or
- *  modify it under the terms of the GNU Lesser General Public License
- *  as published by the Free Software Foundation; either version 2.1 of
- *  the License, or (at your option) any later version.
- *    
- *  This program is distributed in the hope that it will be useful, but
- *  WITHOUT ANY WARRANTY; without even the implied warranty of
- *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
- *  Lesser General Public License for more details.
- *    
- *  You should have received a copy of the GNU Lesser General Public
- *  License along with this program; if not, write to the Free Software
- *  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.commandline;
-
-import java.util.HashMap;
-import java.util.Map;
-
-import net.sf.taverna.t2.commandline.data.SaveResultsHandler;
-import net.sf.taverna.t2.facade.ResultListener;
-import net.sf.taverna.t2.invocation.WorkflowDataToken;
-
-import org.apache.log4j.Logger;
-
-/**
- * A ResultListener that is using for collecting and storing results when running
- * workflows from the commandline.
- * 
- * @author Stuart Owen 
- */
-public class CommandLineResultListener implements ResultListener {
-	
-	private static final Logger logger = Logger.getLogger(CommandLineResultListener.class);
-	
-	private Map<String, WorkflowDataToken> outputMap = new HashMap<String, WorkflowDataToken>();	
-	private Map<String,WorkflowDataToken> finalTokens = new HashMap<String, WorkflowDataToken>();	
-	private final SaveResultsHandler saveResultsHandler;
-	private final int numberOfOutputs;
-	private final boolean saveIndividualResults;
-	private final boolean saveOutputDocument;
-
-	public CommandLineResultListener(int numberOfOutputs,SaveResultsHandler saveResultsHandler,boolean saveIndividualResults,boolean saveOutputDocument) {		
-		this.numberOfOutputs = numberOfOutputs;
-		this.saveResultsHandler = saveResultsHandler;
-		this.saveIndividualResults = saveIndividualResults;
-		this.saveOutputDocument = saveOutputDocument;						
-	}
-
-	public Map<String, WorkflowDataToken> getOutputMap() {
-		return outputMap;
-	}
-
-	public boolean isComplete() {		
-		return finalTokens.size() == numberOfOutputs;
-	}
-
-	public void resultTokenProduced(WorkflowDataToken token, String portName) {		
-		if (saveIndividualResults) {
-			saveResultsHandler.tokenReceived(token, portName);
-		}
-		
-		if (token.isFinal()) {
-			finalTokens.put(portName, token);		
-			if (isComplete() && saveOutputDocument) {
-				try {
-					saveResultsHandler.saveOutputDocument(finalTokens);
-				} catch (Exception e) {
-					logger.error("An error occurred saving the final results to -outputdoc",e);
-				}
-			}
-		}
-	}
-
-}
diff --git a/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/BaclavaDocumentHandler.java b/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/BaclavaDocumentHandler.java
deleted file mode 100644
index e218bc6..0000000
--- a/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/BaclavaDocumentHandler.java
+++ /dev/null
@@ -1,246 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester   
- * 
- *  Modifications to the initial code base are copyright of their
- *  respective authors, or their employers as appropriate.
- * 
- *  This program is free software; you can redistribute it and/or
- *  modify it under the terms of the GNU Lesser General Public License
- *  as published by the Free Software Foundation; either version 2.1 of
- *  the License, or (at your option) any later version.
- *    
- *  This program is distributed in the hope that it will be useful, but
- *  WITHOUT ANY WARRANTY; without even the implied warranty of
- *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
- *  Lesser General Public License for more details.
- *    
- *  You should have received a copy of the GNU Lesser General Public
- *  License along with this program; if not, write to the Free Software
- *  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.commandline.data;
-
-import java.io.File;
-import java.io.FileWriter;
-import java.io.IOException;
-import java.io.PrintWriter;
-import java.net.MalformedURLException;
-import java.net.URL;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-
-import net.sf.taverna.t2.commandline.exceptions.ReadInputException;
-import net.sf.taverna.t2.invocation.InvocationContext;
-import net.sf.taverna.t2.invocation.WorkflowDataToken;
-import net.sf.taverna.t2.reference.DereferenceException;
-import net.sf.taverna.t2.reference.ErrorDocument;
-import net.sf.taverna.t2.reference.IdentifiedList;
-import net.sf.taverna.t2.reference.T2Reference;
-import net.sf.taverna.t2.reference.T2ReferenceType;
-
-import org.apache.log4j.Logger;
-import org.embl.ebi.escience.baclava.DataThing;
-import org.embl.ebi.escience.baclava.factory.DataThingFactory;
-import org.embl.ebi.escience.baclava.factory.DataThingXMLFactory;
-import org.jdom.Document;
-import org.jdom.Element;
-import org.jdom.JDOMException;
-import org.jdom.Namespace;
-import org.jdom.input.SAXBuilder;
-import org.jdom.output.Format;
-import org.jdom.output.XMLOutputter;
-
-/**
- * Handles creating and reading of Baclava documents. 
- * Baclava is a standard originating from Taverna 1.
- * 
- * @author Stuart Owen
- *
- */
-public class BaclavaDocumentHandler {
-
-	private static Namespace namespace = Namespace.getNamespace("b",
-			"http://org.embl.ebi.escience/baclava/0.1alpha");
-
-	private static final Logger logger = Logger
-			.getLogger(BaclavaDocumentHandler.class);
-
-	public Map<String, DataThing> readInputDocument(String inputDocPath)
-			throws ReadInputException {
-		URL url;
-		try {
-			url = new URL("file:");
-		} catch (MalformedURLException e1) {
-			// Should never happen, but just incase:
-			throw new ReadInputException(
-					"The was an internal error setting up the URL to open the inputs. You should contact Taverna support.",
-					e1);
-		}
-		URL inputDocURL;
-		try {
-			inputDocURL = new URL(url, inputDocPath);
-		} catch (MalformedURLException e1) {
-			throw new ReadInputException(
-					"The a error reading the input document from : "
-							+ inputDocPath + ", " + e1.getMessage(), e1);
-		}
-		SAXBuilder builder = new SAXBuilder();
-		Document inputDoc;
-		try {
-			inputDoc = builder.build(inputDocURL.openStream());
-		} catch (IOException e) {
-			throw new ReadInputException(
-					"There was an error reading the input document file: "
-							+ e.getMessage(), e);
-		} catch (JDOMException e) {
-			throw new ReadInputException(
-					"There was a error processing the input document XML: "
-							+ e.getMessage(), e);
-		}
-		Map<String, DataThing> things = DataThingXMLFactory
-				.parseDataDocument(inputDoc);
-		return things;
-	}
-
-	public void storeDocument(Map<String, WorkflowDataToken> finalResults,
-			File outputFile) throws DereferenceException, IOException {
-
-		Map<String, DataThing> dataThings = backDataThingMapFromWorkflowDataTokens(finalResults);
-
-		// Build the string containing the XML document from the result map
-		Document doc = getDataDocument(dataThings);
-		XMLOutputter xo = new XMLOutputter(Format.getPrettyFormat());
-		String xmlString = xo.outputString(doc);
-		PrintWriter out = new PrintWriter(new FileWriter(outputFile));
-		out.print(xmlString);
-		out.flush();
-		out.close();
-	}
-
-	protected Object convertReferencesToObjects(T2Reference reference,
-			InvocationContext context) {
-
-		if (reference.getReferenceType() == T2ReferenceType.ReferenceSet) {
-			// Dereference the object
-			Object dataValue;
-
-			dataValue = context.getReferenceService().renderIdentifier(
-					reference, Object.class, context);			
-			return dataValue;
-
-		} else if (reference.getReferenceType() == T2ReferenceType.ErrorDocument) {
-			// Dereference the ErrorDocument and convert it to some string
-			// representation
-			ErrorDocument errorDocument = (ErrorDocument) context
-					.getReferenceService().resolveIdentifier(reference, null,
-							context);
-			String errorString = ErrorDocumentHandler.buildErrorDocumentString(
-					errorDocument, context);
-			return errorString;
-		} else { // it is an IdentifiedList<T2Reference> - go recursively
-			IdentifiedList<T2Reference> identifiedList = context
-					.getReferenceService().getListService().getList(reference);
-			List<Object> list = new ArrayList<Object>();
-
-			for (int j = 0; j < identifiedList.size(); j++) {
-				T2Reference ref = identifiedList.get(j);
-				list.add(convertReferencesToObjects(ref, context));
-			}
-			return list;
-		}
-	}
-
-	/**
-	 * Returns a org.jdom.Document from a map of port named to DataThingS
-	 * containing the port's results.
-	 */
-	public static Document getDataDocument(Map<String, DataThing> dataThings) {
-		Element rootElement = new Element("dataThingMap", namespace);
-		Document theDocument = new Document(rootElement);
-		for (Iterator<String> i = dataThings.keySet().iterator(); i.hasNext();) {
-			String key = (String) i.next();
-			DataThing value = (DataThing) dataThings.get(key);
-			Element dataThingElement = new Element("dataThing", namespace);
-			dataThingElement.setAttribute("key", key);
-			dataThingElement.addContent(value.getElement());
-			rootElement.addContent(dataThingElement);
-		}
-		return theDocument;
-	}
-
-	/**
-	 * Returns a map of port names to DataThings from a map of port names to a
-	 * list of (lists of ...) result objects.
-	 */
-	protected Map<String, DataThing> bakeDataThingMap(
-			Map<String, Object> resultMap) {
-
-		Map<String, DataThing> dataThingMap = new HashMap<String, DataThing>();
-		for (Iterator<String> i = resultMap.keySet().iterator(); i.hasNext();) {
-			String portName = (String) i.next();
-			dataThingMap.put(portName, DataThingFactory.bake(resultMap
-					.get(portName)));
-		}
-		return dataThingMap;
-	}
-
-	protected Map<String, DataThing> backDataThingMapFromWorkflowDataTokens(
-			Map<String, WorkflowDataToken> tokenMap)
-			throws DereferenceException, IOException {
-		Map<String, DataThing> dataThingMap = new HashMap<String, DataThing>();
-		for (Iterator<String> i = tokenMap.keySet().iterator(); i.hasNext();) {
-			String portName = (String) i.next();
-			WorkflowDataToken token = tokenMap.get(portName);
-			InvocationContext context = token.getContext();
-			List<String> mimeTypeList = new ArrayList<String>();
-
-			if (token.getData().getReferenceType() == T2ReferenceType.ReferenceSet) {
-				
-				mimeTypeList
-						.addAll(MimeTypeHandler.determineMimeTypes(token.getData(), context));				
-				DataThing thingy = DataThingFactory.bake(convertReferencesToObjects(token.getData(), context));
-				thingy.getMetadata().setMIMETypes(mimeTypeList);				
-				dataThingMap.put(portName, thingy);
-				
-			} else if (token.getData().getReferenceType() == T2ReferenceType.ErrorDocument) {
-				
-				DataThing thingy = DataThingFactory.bake(convertReferencesToObjects(token.getData(), context));
-				thingy.getMetadata().addMIMEType("text/plain");
-				dataThingMap.put(portName, thingy);
-				
-			} else {
-				
-				IdentifiedList<T2Reference> identifiedList = context
-						.getReferenceService().getListService().getList(
-								token.getData());
-				List<Object> list = new ArrayList<Object>();
-
-				for (int j = 0; j < identifiedList.size(); j++) {
-					T2Reference ref = identifiedList.get(j);
-					list.add(convertReferencesToObjects(ref, context));
-				}
-
-				// ripple through to get the leaf, to find its mimetype. Seems a
-				// limitation of Baclava
-				// is that the mime-type is set on the entire list, and is not
-				// possible for individual items
-				T2Reference ref = token.getData();
-				while (ref.getReferenceType() != T2ReferenceType.ReferenceSet
-						&& ref.getReferenceType() != T2ReferenceType.ErrorDocument) {
-					identifiedList = context.getReferenceService()
-							.getListService().getList(ref);
-					ref = identifiedList.get(0);
-				}
-				mimeTypeList.addAll(MimeTypeHandler.determineMimeTypes(ref, context));
-				DataThing thingy = DataThingFactory.bake(list);
-				thingy.getMetadata().setMIMETypes(mimeTypeList);
-				dataThingMap.put(portName, thingy);
-				
-			}
-		}
-		return dataThingMap;
-	}	
-}
diff --git a/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/DatabaseConfigurationHandler.java b/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/DatabaseConfigurationHandler.java
deleted file mode 100644
index 174f7e2..0000000
--- a/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/DatabaseConfigurationHandler.java
+++ /dev/null
@@ -1,152 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester   
- * 
- *  Modifications to the initial code base are copyright of their
- *  respective authors, or their employers as appropriate.
- * 
- *  This program is free software; you can redistribute it and/or
- *  modify it under the terms of the GNU Lesser General Public License
- *  as published by the Free Software Foundation; either version 2.1 of
- *  the License, or (at your option) any later version.
- *    
- *  This program is distributed in the hope that it will be useful, but
- *  WITHOUT ANY WARRANTY; without even the implied warranty of
- *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
- *  Lesser General Public License for more details.
- *    
- *  You should have received a copy of the GNU Lesser General Public
- *  License along with this program; if not, write to the Free Software
- *  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.commandline.data;
-import java.io.FileInputStream;
-import java.io.IOException;
-import java.io.InputStream;
-import java.sql.Connection;
-import java.sql.SQLException;
-import java.util.Properties;
-
-import javax.naming.NamingException;
-
-import net.sf.taverna.t2.commandline.exceptions.DatabaseConfigurationException;
-import net.sf.taverna.t2.commandline.options.CommandLineOptions;
-import net.sf.taverna.t2.workbench.reference.config.DataManagementConfiguration;
-import net.sf.taverna.t2.workbench.reference.config.DataManagementHelper;
-
-import org.apache.log4j.Logger;
-
-/**
- * Handles the initialisation and configuration of the data source according to 
- * the command line arguments, or a properties file. 
- * This also handles starting a network based instance of a Derby server, if requested. 
- * 
- * @author Stuart Owen
- *
- */
-public class DatabaseConfigurationHandler {
-
-	private final CommandLineOptions options;
-	private DataManagementConfiguration dbConfig;
-	private static Logger logger = Logger.getLogger(DatabaseConfigurationHandler.class);
-
-	public DatabaseConfigurationHandler(CommandLineOptions options) {
-		this.options = options;
-		dbConfig = DataManagementConfiguration.getInstance();
-		dbConfig.disableAutoSave();
-	}
-
-	public void configureDatabase() throws DatabaseConfigurationException {
-		overrideDefaults();
-		useOptions();
-		if (dbConfig.getStartInternalDerbyServer()) {
-			DataManagementHelper.startDerbyNetworkServer();
-			System.out.println("Started Derby Server on Port: "
-					+ dbConfig.getCurrentPort());
-		}
-		DataManagementHelper.setupDataSource();				
-	}
-
-	public DataManagementConfiguration getDBConfig() {
-		return dbConfig;
-	}
-	
-	private void importConfigurationFromStream(InputStream inStr)
-			throws IOException {
-		Properties p = new Properties();
-		p.load(inStr);		
-		for (Object key : p.keySet()) {
-			dbConfig.setProperty((String)key, p.getProperty((String)key).trim());
-		}
-	}
-
-	protected void overrideDefaults() throws DatabaseConfigurationException {
-		
-		InputStream inStr = DatabaseConfigurationHandler.class.getClassLoader().getResourceAsStream("database-defaults.properties");
-		try {
-			importConfigurationFromStream(inStr);
-		} catch (IOException e) {
-			throw new DatabaseConfigurationException("There was an error reading the default database configuration settings: "+e.getMessage(),e);
-		}
-	}
-
-	protected void readConfigirationFromFile(String filename) throws IOException {
-		FileInputStream fileInputStream = new FileInputStream(filename);
-		importConfigurationFromStream(fileInputStream);
-		fileInputStream.close();
-	}
-
-	public void testDatabaseConnection()
-			throws DatabaseConfigurationException, NamingException, SQLException {
-		//try and get a connection
-		Connection con = null;
-		try {
-			con = DataManagementHelper.openConnection();
-		} finally {
-			if (con!=null)
-				try {
-					con.close();
-				} catch (SQLException e) {
-					logger.warn("There was an SQL error whilst closing the test connection: "+e.getMessage(),e);
-				}
-		}
-	}
-	
-	public void useOptions() throws DatabaseConfigurationException {
-		
-		if (options.hasOption("port")) {			
-			dbConfig.setPort(options.getDatabasePort());		
-		}
-		
-		if (options.hasOption("startdb")) {
-			dbConfig.setStartInternalDerbyServer(true);
-		}
-		
-		if (options.hasOption("inmemory")) {			
-			dbConfig.setInMemory(true);		
-		}
-		
-		if (options.hasOption("embedded")) {
-			dbConfig.setInMemory(false);
-			dbConfig.setDriverClassName("org.apache.derby.jdbc.EmbeddedDriver");
-		}
-		
-		if (options.hasOption("provenance")) {
-			dbConfig.setProvenanceEnabled(true);
-		}
-		
-		if (options.hasOption("clientserver")) {
-			dbConfig.setInMemory(false);
-			dbConfig.setDriverClassName("org.apache.derby.jdbc.ClientDriver");
-			dbConfig.setJDBCUri("jdbc:derby://localhost:" + dbConfig.getPort() + "/t2-database;create=true;upgrade=true");			
-		}		
-		
-		if (options.hasOption("dbproperties")) {
-			try {
-				readConfigirationFromFile(options.getDatabaseProperties());
-			} catch (IOException e) {
-				throw new DatabaseConfigurationException("There was an error reading the database configuration options at "+options.getDatabaseProperties()+" : "+e.getMessage(),e);
-			}
-		}
-	}
-
-}
diff --git a/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/ErrorDocumentHandler.java b/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/ErrorDocumentHandler.java
deleted file mode 100644
index 50b909c..0000000
--- a/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/ErrorDocumentHandler.java
+++ /dev/null
@@ -1,195 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester   
- * 
- *  Modifications to the initial code base are copyright of their
- *  respective authors, or their employers as appropriate.
- * 
- *  This program is free software; you can redistribute it and/or
- *  modify it under the terms of the GNU Lesser General Public License
- *  as published by the Free Software Foundation; either version 2.1 of
- *  the License, or (at your option) any later version.
- *    
- *  This program is distributed in the hope that it will be useful, but
- *  WITHOUT ANY WARRANTY; without even the implied warranty of
- *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
- *  Lesser General Public License for more details.
- *    
- *  You should have received a copy of the GNU Lesser General Public
- *  License along with this program; if not, write to the Free Software
- *  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.commandline.data;
-
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Set;
-
-import javax.swing.tree.DefaultMutableTreeNode;
-
-import net.sf.taverna.t2.invocation.InvocationContext;
-import net.sf.taverna.t2.reference.ErrorDocument;
-import net.sf.taverna.t2.reference.ErrorDocumentService;
-import net.sf.taverna.t2.reference.IdentifiedList;
-import net.sf.taverna.t2.reference.ListService;
-import net.sf.taverna.t2.reference.StackTraceElementBean;
-import net.sf.taverna.t2.reference.T2Reference;
-import net.sf.taverna.t2.reference.T2ReferenceType;
-
-/**
- * Handles Error documents and transforming them into String representations 
- * that can be stored as a file, or within a Baclava document.
- * 
- * @author Stuart Owen
- *
- */
-public class ErrorDocumentHandler {
-
-	/**
-	 * Creates a string representation of the ErrorDocument.
-	 */
-	public static String buildErrorDocumentString(ErrorDocument errDocument,
-			InvocationContext context) {
-
-		String errDocumentString = "";
-
-		String exceptionMessage = errDocument.getExceptionMessage();
-		if (exceptionMessage != null && !exceptionMessage.equals("")) {
-			DefaultMutableTreeNode exceptionMessageNode = new DefaultMutableTreeNode(
-					exceptionMessage);
-			errDocumentString += exceptionMessageNode + "\n";
-			List<StackTraceElementBean> stackTrace = errDocument
-					.getStackTraceStrings();
-			if (stackTrace.size() > 0) {
-				for (StackTraceElementBean stackTraceElement : stackTrace) {
-					errDocumentString += getStackTraceElementString(stackTraceElement)
-							+ "\n";
-				}
-			}
-		}
-
-		Set<T2Reference> errorReferences = errDocument.getErrorReferences();
-		if (!errorReferences.isEmpty()) {
-			errDocumentString += "Set of ErrorDocumentS to follow." + "\n";
-		}
-		int errorCounter = 1;
-		int listCounter = 0;
-		for (T2Reference reference : errorReferences) {
-			if (reference.getReferenceType().equals(
-					T2ReferenceType.ErrorDocument)) {
-				ErrorDocumentService errorDocumentService = context
-						.getReferenceService().getErrorDocumentService();
-				ErrorDocument causeErrorDocument = errorDocumentService
-						.getError(reference);
-				if (listCounter == 0) {
-					errDocumentString += "ErrorDocument " + (errorCounter++)
-							+ "\n";
-				} else {
-					errDocumentString += "ErrorDocument " + listCounter + "."
-							+ (errorCounter++) + "\n";
-				}
-				errDocumentString += buildErrorDocumentString(
-						causeErrorDocument, context)
-						+ "\n";
-			} else if (reference.getReferenceType().equals(
-					T2ReferenceType.IdentifiedList)) {
-				List<ErrorDocument> errorDocuments = getErrorDocuments(
-						reference, context);
-				errDocumentString += "ErrorDocument list " + (++listCounter)
-						+ "\n";
-				for (ErrorDocument causeErrorDocument : errorDocuments) {
-					errDocumentString += buildErrorDocumentString(
-							causeErrorDocument, context)
-							+ "\n";
-				}
-			}
-		}
-
-		return errDocumentString;
-	}
-
-	public static void buildErrorDocumentTree(DefaultMutableTreeNode node,
-			ErrorDocument errorDocument, InvocationContext context) {
-		DefaultMutableTreeNode child = new DefaultMutableTreeNode(errorDocument);
-		String exceptionMessage = errorDocument.getExceptionMessage();
-		if (exceptionMessage != null && !exceptionMessage.equals("")) {
-			DefaultMutableTreeNode exceptionMessageNode = new DefaultMutableTreeNode(
-					exceptionMessage);
-			child.add(exceptionMessageNode);
-			List<StackTraceElementBean> stackTrace = errorDocument
-					.getStackTraceStrings();
-			if (stackTrace.size() > 0) {
-				for (StackTraceElementBean stackTraceElement : stackTrace) {
-					exceptionMessageNode.add(new DefaultMutableTreeNode(
-							getStackTraceElementString(stackTraceElement)));
-				}
-			}
-
-		}
-		node.add(child);
-
-		Set<T2Reference> errorReferences = errorDocument.getErrorReferences();
-		for (T2Reference reference : errorReferences) {
-			if (reference.getReferenceType().equals(
-					T2ReferenceType.ErrorDocument)) {
-				ErrorDocumentService errorDocumentService = context
-						.getReferenceService().getErrorDocumentService();
-				ErrorDocument causeErrorDocument = errorDocumentService
-						.getError(reference);
-				if (errorReferences.size() == 1) {
-					buildErrorDocumentTree(node, causeErrorDocument, context);
-				} else {
-					buildErrorDocumentTree(child, causeErrorDocument, context);
-				}
-			} else if (reference.getReferenceType().equals(
-					T2ReferenceType.IdentifiedList)) {
-				List<ErrorDocument> errorDocuments = getErrorDocuments(
-						reference, context);
-				if (errorDocuments.size() == 1) {
-					buildErrorDocumentTree(node, errorDocuments.get(0), context);
-				} else {
-					for (ErrorDocument errorDocument2 : errorDocuments) {
-						buildErrorDocumentTree(child, errorDocument2, context);
-					}
-				}
-			}
-		}
-	}
-
-	private static String getStackTraceElementString(
-			StackTraceElementBean stackTraceElement) {
-		StringBuilder sb = new StringBuilder();
-		sb.append(stackTraceElement.getClassName());
-		sb.append('.');
-		sb.append(stackTraceElement.getMethodName());
-		if (stackTraceElement.getFileName() == null) {
-			sb.append("(unknown file)");
-		} else {
-			sb.append('(');
-			sb.append(stackTraceElement.getFileName());
-			sb.append(':');
-			sb.append(stackTraceElement.getLineNumber());
-			sb.append(')');
-		}
-		return sb.toString();
-	}
-
-	public static List<ErrorDocument> getErrorDocuments(T2Reference reference,
-			InvocationContext context) {
-		List<ErrorDocument> errorDocuments = new ArrayList<ErrorDocument>();
-		if (reference.getReferenceType().equals(T2ReferenceType.ErrorDocument)) {
-			ErrorDocumentService errorDocumentService = context
-					.getReferenceService().getErrorDocumentService();
-			errorDocuments.add(errorDocumentService.getError(reference));
-		} else if (reference.getReferenceType().equals(
-				T2ReferenceType.IdentifiedList)) {
-			ListService listService = context.getReferenceService()
-					.getListService();
-			IdentifiedList<T2Reference> list = listService.getList(reference);
-			for (T2Reference listReference : list) {
-				errorDocuments
-						.addAll(getErrorDocuments(listReference, context));
-			}
-		}
-		return errorDocuments;
-	}
-}
diff --git a/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/InputsHandler.java b/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/InputsHandler.java
deleted file mode 100644
index f688efb..0000000
--- a/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/InputsHandler.java
+++ /dev/null
@@ -1,235 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester   
- * 
- *  Modifications to the initial code base are copyright of their
- *  respective authors, or their employers as appropriate.
- * 
- *  This program is free software; you can redistribute it and/or
- *  modify it under the terms of the GNU Lesser General Public License
- *  as published by the Free Software Foundation; either version 2.1 of
- *  the License, or (at your option) any later version.
- *    
- *  This program is distributed in the hope that it will be useful, but
- *  WITHOUT ANY WARRANTY; without even the implied warranty of
- *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
- *  Lesser General Public License for more details.
- *    
- *  You should have received a copy of the GNU Lesser General Public
- *  License along with this program; if not, write to the Free Software
- *  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.commandline.data;
-
-import java.io.IOException;
-import java.net.MalformedURLException;
-import java.net.URL;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
-import net.sf.taverna.t2.commandline.exceptions.InputMismatchException;
-import net.sf.taverna.t2.commandline.exceptions.InvalidOptionException;
-import net.sf.taverna.t2.commandline.exceptions.ReadInputException;
-import net.sf.taverna.t2.commandline.options.CommandLineOptions;
-import net.sf.taverna.t2.invocation.InvocationContext;
-import net.sf.taverna.t2.invocation.WorkflowDataToken;
-import net.sf.taverna.t2.reference.T2Reference;
-import net.sf.taverna.t2.workflowmodel.DataflowInputPort;
-
-import org.apache.commons.io.IOUtils;
-import org.apache.log4j.Logger;
-import org.embl.ebi.escience.baclava.DataThing;
-
-/**
- * 
- * Handles the reading, or processing, or input values according to arguments provided to the commandline.
- * The may be either as direct values, from a file, or from a Baclava document.
- * 
- * Also handles registering the input values with the Reference Service, ready to initiate
- * the workflow run.
- * 
- * @author Stuart Owen
- *
- */
-public class InputsHandler {
-	
-	private static Logger logger = Logger.getLogger(InputsHandler.class); 
-
-	
-	public void checkProvidedInputs(Map<String, DataflowInputPort> portMap, CommandLineOptions options) throws InputMismatchException  {
-		//we dont check for the document 
-		if (options.getInputDocument()==null) {
-			Set<String> providedInputNames = new HashSet<String>();
-			for (int i=0;i<options.getInputFiles().length;i+=2) {
-				providedInputNames.add(options.getInputFiles()[i]);								
-			}
-			
-			for (int i=0;i<options.getInputValues().length;i+=2) {
-				providedInputNames.add(options.getInputValues()[i]);								
-			}
-			
-			if (portMap.size()*2 != (options.getInputFiles().length + options.getInputValues().length)) {
-				throw new InputMismatchException("The number of inputs provided does not match the number of input ports.",portMap.keySet(),providedInputNames);
-			}
-			
-			for (String portName : portMap.keySet()) {
-				if (!providedInputNames.contains(portName)) {
-					throw new InputMismatchException("The provided inputs does not contain an input for the port '"+portName+"'",portMap.keySet(),providedInputNames);
-				}
-			}
-		}
-	}
-
-
-	public Map<String, WorkflowDataToken> registerInputs(Map<String, DataflowInputPort> portMap, CommandLineOptions options,
-			InvocationContext context) throws InvalidOptionException, ReadInputException  {
-		Map<String,WorkflowDataToken> inputs = new HashMap<String, WorkflowDataToken>();
-		URL url;
-		try {
-			url = new URL("file:");
-		} catch (MalformedURLException e1) {
-			//Should never happen, but just incase:
-			throw new ReadInputException("The was an internal error setting up the URL to open the inputs. You should contact Taverna support.",e1);
-		}
-				
-		if (options.hasInputFiles()) {
-			String[] inputParams = options.getInputFiles();
-			for (int i = 0; i < inputParams.length; i = i + 2) {
-				String inputName = inputParams[i];
-				try {					
-					URL inputURL = new URL(url, inputParams[i + 1]);
-					DataflowInputPort port = portMap.get(inputName);
-					
-					if (port==null) {
-						throw new InvalidOptionException("Cannot find an input port named '"+inputName+"'");
-					}
-					
-					T2Reference entityId=null;
-					
-					if (options.hasDelimiterFor(inputName)) {
-						String delimiter=options.inputDelimiter(inputName);
-						Object value = IOUtils.toString(inputURL.openStream()).split(delimiter);
-						
-						value=checkForDepthMismatch(1, port.getDepth(), inputName, value);						
-						entityId=context.getReferenceService().register(value, port.getDepth(), true, context);						
-					}
-					else
-					{
-						Object value = IOUtils.toByteArray(inputURL.openStream());
-						value=checkForDepthMismatch(0, port.getDepth(), inputName, value);
-						entityId=context.getReferenceService().register(value, port.getDepth(), true, context);
-					}
-															
-					WorkflowDataToken token = new WorkflowDataToken("",new int[]{}, entityId, context);
-					inputs.put(inputName, token);
-					
-				} catch (IndexOutOfBoundsException e) {
-					throw new InvalidOptionException("Missing input filename for input "+ inputName);					
-				} catch (IOException e) {
-					throw new InvalidOptionException("Could not read input " + inputName + ": " + e.getMessage());				
-				}
-			}
-		}
-		
-		if (options.hasInputValues()) {
-			String[] inputParams = options.getInputValues();
-			for (int i = 0; i < inputParams.length; i = i + 2) {
-				String inputName = inputParams[i];
-				try {					
-					String inputValue = inputParams[i + 1];
-					DataflowInputPort port = portMap.get(inputName);
-					
-					if (port==null) {
-						throw new InvalidOptionException("Cannot find an input port named '"+inputName+"'");
-					}
-										
-					T2Reference entityId=null;
-					if (options.hasDelimiterFor(inputName)) {
-						String delimiter=options.inputDelimiter(inputName);
-						Object value=checkForDepthMismatch(1, port.getDepth(), inputName, inputValue.split(delimiter));
-						entityId=context.getReferenceService().register(value, port.getDepth(), true, context);						
-					}
-					else
-					{
-						Object value=checkForDepthMismatch(0, port.getDepth(), inputName, inputValue);
-						entityId=context.getReferenceService().register(value, port.getDepth(), true, context);
-					}
-										
-					WorkflowDataToken token = new WorkflowDataToken("",new int[]{}, entityId, context);								
-					inputs.put(inputName, token);					
-					
-				} catch (IndexOutOfBoundsException e) {
-					throw new InvalidOptionException("Missing input value for input "+ inputName);					
-				} 
-			}
-			
-		}
-		
-		if (options.getInputDocument()!=null) {
-			String inputDocPath = options.getInputDocument();
-			Map<String, DataThing> things = new BaclavaDocumentHandler().readInputDocument(inputDocPath);
-			for (String inputName : things.keySet()) {
-				DataThing thing = things.get(inputName);
-				Object object = thing.getDataObject();
-				T2Reference entityId=context.getReferenceService().register(object,getObjectDepth(object), true, context);
-				WorkflowDataToken token = new WorkflowDataToken("",new int[]{}, entityId, context);
-				inputs.put(inputName, token);
-			}
-		}
-		
-		return inputs;
-	}
-	
-	private Object checkForDepthMismatch(int inputDepth,int portDepth,String inputName,Object inputValue) throws InvalidOptionException {
-		if (inputDepth!=portDepth) {
-			if (inputDepth<portDepth) {
-				logger.warn("Wrapping input for '" + inputName + "' from a depth of "+inputDepth+" to the required depth of "+portDepth);
-				while (inputDepth<portDepth) {
-					List<Object> l=new ArrayList<Object>();
-					l.add(inputValue);
-					inputValue=l;
-					inputDepth++;
-				}
-			}
-			else {
-				String msg="There is a mismatch between depth of the list for the input port '"+inputName+"' and the data presented. The input port requires a "+depthToString(portDepth)+" and the data presented is a "+depthToString(inputDepth);				
-				throw new InvalidOptionException(msg);
-			}
-		}
-		
-		return inputValue;
-	}
-	
-	private String depthToString(int depth) {
-		switch (depth) {
-		case 0:
-			return "single item";			
-		case 1:
-			return "list";			
-		case 2:
-			return "list of lists";			
-		default:
-			return "list of depth "+depth;
-		}
-	}
-
-
-	@SuppressWarnings("unchecked")
-	private int getObjectDepth(Object o) {
-		int result = 0;
-		if (o instanceof Iterable) {
-			result++;
-			Iterator i = ((Iterable) o).iterator();
-			
-			if (i.hasNext()) {
-				Object child = i.next();
-				result = result + getObjectDepth(child);
-			}
-		}
-		return result;
-	}
-}
diff --git a/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/MimeTypeHandler.java b/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/MimeTypeHandler.java
deleted file mode 100644
index 2e026d6..0000000
--- a/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/MimeTypeHandler.java
+++ /dev/null
@@ -1,123 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester   
- * 
- *  Modifications to the initial code base are copyright of their
- *  respective authors, or their employers as appropriate.
- * 
- *  This program is free software; you can redistribute it and/or
- *  modify it under the terms of the GNU Lesser General Public License
- *  as published by the Free Software Foundation; either version 2.1 of
- *  the License, or (at your option) any later version.
- *    
- *  This program is distributed in the hope that it will be useful, but
- *  WITHOUT ANY WARRANTY; without even the implied warranty of
- *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
- *  Lesser General Public License for more details.
- *    
- *  You should have received a copy of the GNU Lesser General Public
- *  License along with this program; if not, write to the Free Software
- *  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.commandline.data;
-
-import java.io.IOException;
-import java.io.InputStream;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.List;
-
-import net.sf.taverna.t2.invocation.InvocationContext;
-import net.sf.taverna.t2.reference.ExternalReferenceSPI;
-import net.sf.taverna.t2.reference.ReferenceSet;
-import net.sf.taverna.t2.reference.ReferencedDataNature;
-import net.sf.taverna.t2.reference.T2Reference;
-import net.sf.taverna.t2.reference.T2ReferenceType;
-
-import org.apache.log4j.Logger;
-
-import eu.medsea.mimeutil.MimeType;
-import eu.medsea.mimeutil.MimeUtil2;
-
-/**
- * Handles identifying mime-types for a given data stream, or T2Reference
- * 
- * @author Stuart Owen 
- */
-public class MimeTypeHandler {
-	
-	private static Logger logger = Logger.getLogger(MimeTypeHandler.class);
-	
-	@SuppressWarnings("unchecked")
-	public static List<MimeType> getMimeTypes(InputStream inputStream,InvocationContext context) throws IOException {
-		List<MimeType> mimeList = new ArrayList<MimeType>();
-		MimeUtil2 mimeUtil = new MimeUtil2();
-		mimeUtil
-				.registerMimeDetector("eu.medsea.mimeutil.detector.ExtensionMimeDetector");
-		mimeUtil
-				.registerMimeDetector("eu.medsea.mimeutil.detector.MagicMimeMimeDetector");
-		mimeUtil
-				.registerMimeDetector("eu.medsea.mimeutil.detector.WindowsRegistryMimeDetector");
-		mimeUtil
-				.registerMimeDetector("eu.medsea.mimeutil.detector.ExtraMimeTypes");
-		
-		try {
-			byte[] bytes = new byte[2048];
-			inputStream.read(bytes);
-			Collection mimeTypes2 = mimeUtil.getMimeTypes(bytes);
-			mimeList.addAll(mimeTypes2);
-		} finally {
-			try {
-				inputStream.close();
-			} catch (IOException e) {
-				logger.error(
-						"Failed to close stream after determining mimetype", e);
-			}
-		}
-		return mimeList;
-	}
-	
-	public static List<String> determineMimeTypes(T2Reference reference,
-			InvocationContext context) throws IOException {
-		List<String> mimeTypeList = new ArrayList<String>();
-
-		if (reference.getReferenceType() == T2ReferenceType.ErrorDocument) {
-			mimeTypeList.add("text/plain");
-		} else {
-			ReferenceSet referenceSet = (ReferenceSet) context
-			.getReferenceService().resolveIdentifier(reference,
-					null, context);
-			if (!referenceSet.getExternalReferences().isEmpty()) {
-				
-				ExternalReferenceSPI externalReference = referenceSet
-						.getExternalReferences().iterator().next();
-
-				List<MimeType> mimeTypes = getMimeTypes(
-						externalReference.openStream(context), context);
-
-				for (MimeType type : mimeTypes) {
-					if (!type.toString().equals("text/plain")
-							&& !type.toString().equals(
-									"application/octet-stream")) {
-						mimeTypeList.add(type.toString());
-					}
-				}
-				if (externalReference.getDataNature() == ReferencedDataNature.TEXT) {
-					mimeTypeList.add("text/plain");
-				} else {
-					mimeTypeList.add("application/octet-stream");
-				}
-			}
-
-		}
-
-		return mimeTypeList;
-	}
-		
-	public static List<MimeType> getMimeTypes(
-			ExternalReferenceSPI externalReference, InvocationContext context) throws IOException {
-		
-		InputStream inputStream = externalReference.openStream(context);
-		return getMimeTypes(inputStream, context);
-	}
-
-}
diff --git a/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/SaveResultsHandler.java b/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/SaveResultsHandler.java
deleted file mode 100644
index a5b20a1..0000000
--- a/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/SaveResultsHandler.java
+++ /dev/null
@@ -1,241 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester   
- * 
- *  Modifications to the initial code base are copyright of their
- *  respective authors, or their employers as appropriate.
- * 
- *  This program is free software; you can redistribute it and/or
- *  modify it under the terms of the GNU Lesser General Public License
- *  as published by the Free Software Foundation; either version 2.1 of
- *  the License, or (at your option) any later version.
- *    
- *  This program is distributed in the hope that it will be useful, but
- *  WITHOUT ANY WARRANTY; without even the implied warranty of
- *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
- *  Lesser General Public License for more details.
- *    
- *  You should have received a copy of the GNU Lesser General Public
- *  License along with this program; if not, write to the Free Software
- *  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.commandline.data;
-
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.OutputStreamWriter;
-import java.io.PrintWriter;
-import java.util.HashMap;
-import java.util.Map;
-
-import net.sf.taverna.t2.commandline.CommandLineResultListener;
-import net.sf.taverna.t2.invocation.InvocationContext;
-import net.sf.taverna.t2.invocation.WorkflowDataToken;
-import net.sf.taverna.t2.reference.ErrorDocument;
-import net.sf.taverna.t2.reference.ExternalReferenceSPI;
-import net.sf.taverna.t2.reference.Identified;
-import net.sf.taverna.t2.reference.IdentifiedList;
-import net.sf.taverna.t2.reference.ReferenceSet;
-import net.sf.taverna.t2.reference.T2Reference;
-import net.sf.taverna.t2.reference.T2ReferenceType;
-
-import org.apache.log4j.Logger;
-
-/**
- * Handles all recording of results as they are received by the {@link CommandLineResultListener}
- * or when the workflow enactment has completed.
- * This includes saving as a Baclava Document, or storing individual results.
- * 
- * @author Stuart Owen
- * @see BaclavaDocumentHandler
- * @see CommandLineResultListener
- *
- */
-public class SaveResultsHandler {
-
-	private final Map<String, Integer> portsAndDepth;
-	private HashMap<String, Integer> depthSeen;
-	private final File rootDirectory;
-	private static Logger logger = Logger
-			.getLogger(CommandLineResultListener.class);
-	private final File outputDocumentFile;	
-
-	public SaveResultsHandler(Map<String, Integer> portsAndDepth,
-			File rootDirectory, File outputDocumentFile) {
-
-		this.portsAndDepth = portsAndDepth;
-		this.rootDirectory = rootDirectory;
-		this.outputDocumentFile = outputDocumentFile;
-
-		depthSeen = new HashMap<String, Integer>();
-		for (String portName : portsAndDepth.keySet()) {
-			depthSeen.put(portName, -1);
-		}
-	}
-
-	public void tokenReceived(WorkflowDataToken token, String portName) {
-		if (rootDirectory != null) { //only save individual results if a directory is specified
-			if (portsAndDepth.containsKey(portName)) {
-				int[] index = token.getIndex();
-				if (depthSeen.get(portName) == -1)
-					depthSeen.put(portName, index.length);
-				if (index.length >= depthSeen.get(portName)) {
-					storeToken(token, portName);
-				}
-			} else {
-				logger
-						.error("Result recieved for unexpected Port: "
-								+ portName);
-			}
-		}
-	}
-	
-	public void saveOutputDocument(Map<String,WorkflowDataToken> allResults) throws Exception {
-		if (outputDocumentFile!=null) {
-			new BaclavaDocumentHandler().storeDocument(allResults, outputDocumentFile);
-		}
-	}
-
-	protected void storeToken(WorkflowDataToken token, String portName) {
-
-		if (token.getData().getReferenceType() == T2ReferenceType.IdentifiedList) {
-			saveList(token, portName);
-		} else {
-			File dataDirectory = rootDirectory;
-			File dataFile = null;
-
-			if (token.getIndex().length > 0) {
-				dataDirectory = new File(rootDirectory, portName);
-				for (int i = 0; i < token.getIndex().length - 1; i++) {
-					dataDirectory = new File(dataDirectory, String
-							.valueOf(token.getIndex()[i] + 1));
-				}
-				dataFile = new File(dataDirectory, String.valueOf(token
-						.getIndex()[token.getIndex().length - 1] + 1));
-			} else {
-				dataFile = new File(dataDirectory, portName);
-			}
-			
-			if (!dataDirectory.exists()) {
-				dataDirectory.mkdirs();
-			}
-
-			if (dataFile.exists()) {
-				System.err.println("There is already data saved to: "
-						+ dataFile.getAbsolutePath());
-				System.exit(-1);
-			}
-			
-			saveIndividualDataFile(token.getData(), dataFile, token
-					.getContext());
-		}
-	}
-
-	private void saveList(WorkflowDataToken token, String portName) {
-		File dataDirectory = null;
-		int[] index = token.getIndex();
-
-		if (index.length > 0) {
-			dataDirectory = new File(rootDirectory, portName);
-			for (int i = 0; i < index.length - 1; i++) {
-				dataDirectory = new File(dataDirectory, String.valueOf(token
-						.getIndex()[i] + 1));
-			}
-			dataDirectory = new File(dataDirectory, String.valueOf(token
-					.getIndex()[index.length - 1]+ 1));
-		} else {
-			dataDirectory = new File(rootDirectory, portName);
-		}
-		
-		T2Reference reference = token.getData();
-		IdentifiedList<T2Reference> list = token.getContext()
-				.getReferenceService().getListService().getList(reference);
-		saveListItems(token.getContext(), dataDirectory,  list);
-	}
-
-	private void saveListItems(InvocationContext context, File dataDirectory,IdentifiedList<T2Reference> list) {
-		int c = 0;
-		if (!dataDirectory.exists()) {
-			dataDirectory.mkdirs();
-		}
-		for (T2Reference id : list) {			
-			File dataFile = new File(dataDirectory, String.valueOf(c+1));
-			if (id.getReferenceType() ==  T2ReferenceType.IdentifiedList) {
-				IdentifiedList<T2Reference> innerList = context
-				.getReferenceService().getListService().getList(id);				
-				saveListItems(context, dataFile, innerList);
-			}
-			else {				
-				saveIndividualDataFile(id, dataFile, context);				
-			}
-			c++;
-		}
-	}
-
-	protected void saveIndividualDataFile(T2Reference reference, File dataFile,
-			InvocationContext context) {
-
-		if (dataFile.exists()) {
-			System.err.println("There is already data saved to: "
-					+ dataFile.getAbsolutePath());
-			System.exit(-1);
-		}
-
-		Object data = null;
-		if (reference.containsErrors()) {
-			ErrorDocument errorDoc = context.getReferenceService()
-			.getErrorDocumentService().getError(reference);
-			data = ErrorDocumentHandler.buildErrorDocumentString(errorDoc, context);
-			dataFile = new File(dataFile.getAbsolutePath()+".error");
-		} else {
-			// FIXME: this really should be done using a stream rather
-			// than an instance of the object in memory			
-			
-			Identified identified = context.getReferenceService().resolveIdentifier(reference, null, context);
-			ReferenceSet referenceSet = (ReferenceSet) identified;
-			
-			if (referenceSet.getExternalReferences().isEmpty()) {
-				data = context.getReferenceService().renderIdentifier(reference,
-						Object.class, context);
-			}
-			else {
-				ExternalReferenceSPI externalReference = referenceSet.getExternalReferences().iterator().next();				
-				data = externalReference.openStream(context);
-			}			
-		}
-
-		FileOutputStream fos;
-		try {
-			fos = new FileOutputStream(dataFile);
-			if (data instanceof InputStream) {			
-				InputStream inStream = (InputStream)data;
-				int c;
-				while ( ( c = inStream.read() ) != -1  ) {
-					fos.write( (char) c);
-				}				
-				fos.flush();
-				fos.close();
-			}
-			if (data instanceof byte[]) {
-				fos.write((byte[]) data);
-				fos.flush();
-				fos.close();
-			} else {
-				PrintWriter out = new PrintWriter(new OutputStreamWriter(fos));
-				out.print(data.toString());
-				out.flush();
-				out.close();
-			}
-		} catch (FileNotFoundException e) {
-			logger.error("Unable to find the file: '"
-					+ dataFile.getAbsolutePath() + "' for writing results", e);
-		} catch (IOException e) {
-			logger.error("IO Error writing resuts to: '"
-					+ dataFile.getAbsolutePath(), e);
-		}
-	}
-	
-	
-}
diff --git a/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/exceptions/DatabaseConfigurationException.java b/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/exceptions/DatabaseConfigurationException.java
deleted file mode 100644
index 616fb70..0000000
--- a/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/exceptions/DatabaseConfigurationException.java
+++ /dev/null
@@ -1,43 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester   
- * 
- *  Modifications to the initial code base are copyright of their
- *  respective authors, or their employers as appropriate.
- * 
- *  This program is free software; you can redistribute it and/or
- *  modify it under the terms of the GNU Lesser General Public License
- *  as published by the Free Software Foundation; either version 2.1 of
- *  the License, or (at your option) any later version.
- *    
- *  This program is distributed in the hope that it will be useful, but
- *  WITHOUT ANY WARRANTY; without even the implied warranty of
- *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
- *  Lesser General Public License for more details.
- *    
- *  You should have received a copy of the GNU Lesser General Public
- *  License along with this program; if not, write to the Free Software
- *  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.commandline.exceptions;
-
-public class DatabaseConfigurationException extends Exception {
-	
-	private static final long serialVersionUID = -4128248547532355697L;
-
-	public DatabaseConfigurationException() {
-
-	}
-
-	public DatabaseConfigurationException(String message) {
-		super(message);
-	}
-
-	public DatabaseConfigurationException(Throwable cause) {
-		super(cause);
-	}
-
-	public DatabaseConfigurationException(String message, Throwable cause) {
-		super(message, cause);
-	}
-
-}
diff --git a/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/exceptions/InputMismatchException.java b/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/exceptions/InputMismatchException.java
deleted file mode 100644
index eb4a289..0000000
--- a/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/exceptions/InputMismatchException.java
+++ /dev/null
@@ -1,54 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester   
- * 
- *  Modifications to the initial code base are copyright of their
- *  respective authors, or their employers as appropriate.
- * 
- *  This program is free software; you can redistribute it and/or
- *  modify it under the terms of the GNU Lesser General Public License
- *  as published by the Free Software Foundation; either version 2.1 of
- *  the License, or (at your option) any later version.
- *    
- *  This program is distributed in the hope that it will be useful, but
- *  WITHOUT ANY WARRANTY; without even the implied warranty of
- *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
- *  Lesser General Public License for more details.
- *    
- *  You should have received a copy of the GNU Lesser General Public
- *  License along with this program; if not, write to the Free Software
- *  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.commandline.exceptions;
-
-import java.util.Set;
-
-public class InputMismatchException extends InvalidOptionException {	
-	
-	private static final long serialVersionUID = -5368068332397293706L;
-	private final Set<String> expectedInputNames;
-	private final Set<String> providedInputNames;
-	
-	public InputMismatchException(String msg, Set<String> expectedInputNames, Set<String> providedInputNames) {
-		super(msg);
-		this.expectedInputNames = expectedInputNames;
-		this.providedInputNames = providedInputNames;				
-	}
-
-	public String getMessage() {
-		String result = super.getMessage();
-		result += "\n" + expectedInputNames.size() + " inputs were expected";
-		if (expectedInputNames.size()>0) result += " which are:\n";
-		for (String name : expectedInputNames) {
-			result += "'"+name+"' ";			
-		}
-		
-		result += "\n" + providedInputNames.size() + " inputs were provided";
-		if (providedInputNames.size()>0) result += " which are:\n";
-		for (String name : providedInputNames) {
-			result += "'"+name+"' ";			
-		}
-		return result;
-	}
-	
-
-}
diff --git a/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/exceptions/InvalidOptionException.java b/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/exceptions/InvalidOptionException.java
deleted file mode 100644
index c07a19f..0000000
--- a/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/exceptions/InvalidOptionException.java
+++ /dev/null
@@ -1,30 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester   
- * 
- *  Modifications to the initial code base are copyright of their
- *  respective authors, or their employers as appropriate.
- * 
- *  This program is free software; you can redistribute it and/or
- *  modify it under the terms of the GNU Lesser General Public License
- *  as published by the Free Software Foundation; either version 2.1 of
- *  the License, or (at your option) any later version.
- *    
- *  This program is distributed in the hope that it will be useful, but
- *  WITHOUT ANY WARRANTY; without even the implied warranty of
- *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
- *  Lesser General Public License for more details.
- *    
- *  You should have received a copy of the GNU Lesser General Public
- *  License along with this program; if not, write to the Free Software
- *  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.commandline.exceptions;
-
-public class InvalidOptionException extends Exception {
-
-	private static final long serialVersionUID = 2467409785164223258L;
-
-	public InvalidOptionException(String message) {
-		super(message);
-	}
-}
diff --git a/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/exceptions/OpenDataflowException.java b/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/exceptions/OpenDataflowException.java
deleted file mode 100644
index 664ab71..0000000
--- a/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/exceptions/OpenDataflowException.java
+++ /dev/null
@@ -1,44 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester   
- * 
- *  Modifications to the initial code base are copyright of their
- *  respective authors, or their employers as appropriate.
- * 
- *  This program is free software; you can redistribute it and/or
- *  modify it under the terms of the GNU Lesser General Public License
- *  as published by the Free Software Foundation; either version 2.1 of
- *  the License, or (at your option) any later version.
- *    
- *  This program is distributed in the hope that it will be useful, but
- *  WITHOUT ANY WARRANTY; without even the implied warranty of
- *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
- *  Lesser General Public License for more details.
- *    
- *  You should have received a copy of the GNU Lesser General Public
- *  License along with this program; if not, write to the Free Software
- *  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.commandline.exceptions;
-
-public class OpenDataflowException extends Exception {
-
-	
-	private static final long serialVersionUID = 4778578311101082197L;
-
-	public OpenDataflowException() {
-		
-	}
-
-	public OpenDataflowException(String message) {
-		super(message);	
-	}
-
-	public OpenDataflowException(Throwable cause) {
-		super(cause);
-	}
-
-	public OpenDataflowException(String message, Throwable cause) {
-		super(message, cause);
-	}
-
-}
diff --git a/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/exceptions/ReadInputException.java b/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/exceptions/ReadInputException.java
deleted file mode 100644
index 226d6ea..0000000
--- a/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/exceptions/ReadInputException.java
+++ /dev/null
@@ -1,35 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester   
- * 
- *  Modifications to the initial code base are copyright of their
- *  respective authors, or their employers as appropriate.
- * 
- *  This program is free software; you can redistribute it and/or
- *  modify it under the terms of the GNU Lesser General Public License
- *  as published by the Free Software Foundation; either version 2.1 of
- *  the License, or (at your option) any later version.
- *    
- *  This program is distributed in the hope that it will be useful, but
- *  WITHOUT ANY WARRANTY; without even the implied warranty of
- *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
- *  Lesser General Public License for more details.
- *    
- *  You should have received a copy of the GNU Lesser General Public
- *  License along with this program; if not, write to the Free Software
- *  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.commandline.exceptions;
-
-public class ReadInputException extends Exception {
-		
-	private static final long serialVersionUID = -3494432791254643055L;
-
-	public ReadInputException(String msg) {
-		super(msg); 
-	}
-	
-	public ReadInputException(String msg, Throwable e) {
-		super(msg,e); 
-	}
-	
-}
diff --git a/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/options/CommandLineOptions.java b/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/options/CommandLineOptions.java
deleted file mode 100644
index 07a6cce..0000000
--- a/taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/options/CommandLineOptions.java
+++ /dev/null
@@ -1,399 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester   
- * 
- *  Modifications to the initial code base are copyright of their
- *  respective authors, or their employers as appropriate.
- * 
- *  This program is free software; you can redistribute it and/or
- *  modify it under the terms of the GNU Lesser General Public License
- *  as published by the Free Software Foundation; either version 2.1 of
- *  the License, or (at your option) any later version.
- *    
- *  This program is distributed in the hope that it will be useful, but
- *  WITHOUT ANY WARRANTY; without even the implied warranty of
- *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
- *  Lesser General Public License for more details.
- *    
- *  You should have received a copy of the GNU Lesser General Public
- *  License along with this program; if not, write to the Free Software
- *  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.commandline.options;
-
-import java.io.IOException;
-import java.io.InputStream;
-
-import net.sf.taverna.t2.commandline.exceptions.InvalidOptionException;
-
-import org.apache.commons.cli.CommandLine;
-import org.apache.commons.cli.CommandLineParser;
-import org.apache.commons.cli.GnuParser;
-import org.apache.commons.cli.HelpFormatter;
-import org.apache.commons.cli.Option;
-import org.apache.commons.cli.OptionBuilder;
-import org.apache.commons.cli.Options;
-import org.apache.commons.cli.ParseException;
-import org.apache.commons.io.IOUtils;
-import org.apache.log4j.Logger;
-
-/**
- * Handles the processing of command line arguments for enacting a workflow.
- * This class encapsulates all command line options, and exposes them through higher-level
- * accessors. Upon creation it checks the validity of the command line options and raises an
- * {@link InvalidOptionException} if they are invalid.
- * 
- * @author Stuart Owen
- *
- */
-public class CommandLineOptions {
-
-	private static final Logger logger = Logger
-			.getLogger(CommandLineOptions.class);
-	private Options options;
-	private CommandLine commandLine;
-
-	public CommandLineOptions(String[] args) throws InvalidOptionException {
-		this.options = intitialiseOptions();
-		this.commandLine = processArgs(args);		
-		checkForInvalid();
-	}
-
-	public boolean askedForHelp() {
-		return hasOption("help") || (getArgs().length==0 && getOptions().length==0);
-	}
-
-	protected void checkForInvalid() throws InvalidOptionException {
-		if (askedForHelp()) return;
-		if (hasOption("provenance")
-				&& !(hasOption("embedded") || hasOption("clientserver") || hasOption("dbproperties")))
-			throw new InvalidOptionException(
-					"You should be running with a database to use provenance");
-		if (hasOption("provenance") && hasOption("inmemory"))
-			throw new InvalidOptionException(
-					"You should be running with a database to use provenance");
-		if ((hasOption("inputfile") || hasOption("inputvalue"))
-				&& hasOption("inputdoc"))
-			throw new InvalidOptionException(
-					"You can't provide both -input and -inputdoc arguments");
-		
-		if (hasOption("inputdelimiter") && hasOption("inputdoc"))
-			throw new InvalidOptionException("You cannot combine the -inputdelimiter and -inputdoc arguments");
-
-		if (getArgs().length == 0
-				&& !(hasOption("help") || hasOption("startdb")))
-			throw new InvalidOptionException("You must specify a workflow");
-		
-		if (hasOption("inmemory") && hasOption("embedded"))
-			throw new InvalidOptionException(
-					"The options -embedded, -clientserver and -inmemory cannot be used together");
-		if (hasOption("inmemory") && hasOption("clientserver"))
-			throw new InvalidOptionException(
-					"The options -embedded, -clientserver and -inmemory cannot be used together");
-		if (hasOption("embedded") && hasOption("clientserver"))
-			throw new InvalidOptionException(
-					"The options -embedded, -clientserver and -inmemory cannot be used together");
-	}
-
-	public void displayHelp() {
-		boolean full = false;
-		if (hasOption("help")) full=true;
-		displayHelp(full);
-	}
-
-	public void displayHelp(boolean showFullText) {
-
-		HelpFormatter formatter = new HelpFormatter();
-		try {
-			formatter
-					.printHelp("executeworkflow [options] [workflow]", options);
-			if (showFullText) {
-				InputStream helpStream = CommandLineOptions.class
-						.getClassLoader().getResourceAsStream("help.txt");
-				String helpText = IOUtils.toString(helpStream);
-				System.out.println(helpText);
-			}
-
-		} catch (IOException e) {
-			logger.error("Error reading the help document", e);
-			System.exit(-1);
-		}
-	}
-
-	public String[] getArgs() {
-		return commandLine.getArgs();
-	}		
-	
-	/**
-	 * 
-	 * @return the port that the database should run on
-	 */
-	public String getDatabasePort() {
-		return getOptionValue("port");
-	}
-
-	/**
-	 * 
-	 * @return a path to a properties file that contains database configuration
-	 *         settings
-	 */
-	public String getDatabaseProperties() {
-		return getOptionValue("dbproperties");
-	}
-
-	/**
-	 * 
-	 * @return the path to the input document
-	 */
-	public String getInputDocument() {
-		return getOptionValue("inputdoc");
-	}
-
-	/**
-	 * Returns an array that alternates between a portname and path to a file
-	 * containing the input values. Therefore the array will always contain an
-	 * even number of elements
-	 * 
-	 * @return an array of portname and path to files containing individual
-	 *         inputs.
-	 */
-	public String[] getInputFiles() {
-		if (hasInputFiles()) {
-			return getOptionValues("inputfile");
-		} else {
-			return new String[] {};
-		}
-	}
-
-	public String[] getInputValues() {
-		if (hasInputValues()) {
-			return getOptionValues("inputvalue");
-		} else {
-			return new String[] {};
-		}
-	}
-
-	public String getLogFile() {
-		return getOptionValue("logfile");
-	}
-
-	public Option [] getOptions() {
-		return commandLine.getOptions();
-	}
-
-	private String getOptionValue(String opt) {
-		return commandLine.getOptionValue(opt);
-	}
-
-	private String[] getOptionValues(String arg0) {
-		return commandLine.getOptionValues(arg0);
-	}
-
-	/**
-	 * 
-	 * @return the directory to write the results to
-	 */
-	public String getOutputDirectory() {
-		return getOptionValue("outputdir");
-	}
-
-	/**
-	 * 
-	 * @return the path to the output document
-	 */
-	public String getOutputDocument() {
-		return getOptionValue("outputdoc");
-	}
-
-	public boolean getStartDatabase() {
-		return hasOption("startdb");
-	}
-
-	public boolean getStartDatabaseOnly() throws InvalidOptionException {
-		return (getStartDatabase() && (getWorkflow() == null));
-	}
-
-	public String getWorkflow() throws InvalidOptionException {
-		if (getArgs().length == 0) {
-			return null;
-		} else if (getArgs().length != 1) {
-			throw new InvalidOptionException(
-					"You should only specify one workflow file");
-		} else {
-			return getArgs()[0];
-		}
-	}
-
-	public boolean hasDelimiterFor(String inputName) {
-		boolean result = false;
-		if (hasOption("inputdelimiter")) {
-			String [] values = getOptionValues("inputdelimiter");
-			for (int i=0;i<values.length;i+=2) {
-				if (values[i].equals(inputName))
-				{
-					result=true;
-					break;
-				}
-			}
-		}
-		return result;
-	}
-
-	public boolean hasInputFiles() {
-		return hasOption("inputfile");
-	}
-
-	public boolean hasInputValues() {
-		return hasOption("inputvalue");
-	}
-
-	public boolean hasLogFile() {
-		return hasOption("logfile");
-	}
-
-	public boolean hasOption(String option) {
-		return commandLine.hasOption(option);
-	}
-
-	public String inputDelimiter(String inputName) {
-		String result = null;
-		if (hasOption("inputdelimiter")) {
-			String [] values = getOptionValues("inputdelimiter");
-			for (int i=0;i<values.length;i+=2) {
-				if (values[i].equals(inputName))
-				{
-					result=values[i+1];
-					break;
-				}
-			}
-		}
-		return result;
-	}
-
-	@SuppressWarnings("static-access")
-	private Options intitialiseOptions() {
-		Option helpOption = new Option("help", "displays comprehensive help information");
-
-		Option outputOption = OptionBuilder
-				.withArgName("directory")
-				.hasArg()
-				.withDescription(
-						"save outputs as files in directory, default "
-								+ "is to make a new directory workflowName_output")
-				.create("outputdir");
-
-		Option outputdocOption = OptionBuilder.withArgName("document").hasArg()
-				.withDescription("save outputs to a new Baclava document")
-				.create("outputdoc");
-
-		Option logFileOption = OptionBuilder
-				.withArgName("filename")
-				.hasArg()
-				.withDescription(
-						"the logfile to which more verbose logging will be written to")
-				.create("logfile");
-
-		Option inputdocOption = OptionBuilder.withArgName("document").hasArg()
-				.withDescription("load inputs from a Baclava document").create(
-						"inputdoc");
-
-		Option inputFileOption = OptionBuilder
-				.withArgName("inputname filename").hasArgs(2)
-				.withValueSeparator(' ').withDescription(
-						"load the named input from file or URL").create(
-						"inputfile");
-
-		Option inputValueOption = OptionBuilder.withArgName("inputname value")
-				.hasArgs(2).withValueSeparator(' ').withDescription(
-						"directly use the value for the named input").create(
-						"inputvalue");
-
-		Option inputDelimiterOption = OptionBuilder
-				.withArgName("inputname delimiter")
-				.hasArgs(2)
-				.withValueSeparator(' ')
-				.withDescription(
-						"causes an inputvalue or inputfile to be split into a list according to the delimiter. The associated workflow input must be expected to receive a list")
-				.create("inputdelimiter");
-
-		Option dbProperties = OptionBuilder.withArgName("filename").hasArg()
-				.withDescription(
-						"loads a properties file to configure the database")
-				.create("dbproperties");
-
-		Option port = OptionBuilder
-				.withArgName("portnumber")
-				.hasArg()
-				.withDescription(
-						"the port that the database is running on. If set requested to start its own internal server, this is the start port that will be used.")
-				.create("port");
-
-		Option embedded = new Option("embedded",
-				"connects to an embedded Derby database. This can prevent mulitple invocations");
-		Option clientserver = new Option("clientserver",
-				"connects as a client to a derby server instance.");
-		Option inMemOption = new Option(
-				"inmemory",
-				"runs the workflow with data stored in-memory rather than in a database. This can give performance inprovements, at the cost of overall memory usage");
-		Option startDB = new Option("startdb",
-				"automatically starts an internal Derby database server.");
-		Option provenance = new Option("provenance",
-				"generates provenance information and stores it in the database.");
-
-		Options options = new Options();
-		options.addOption(helpOption);
-		options.addOption(inputFileOption);
-		options.addOption(inputValueOption);
-		options.addOption(inputDelimiterOption);
-		options.addOption(inputdocOption);
-		options.addOption(outputOption);
-		options.addOption(outputdocOption);
-		options.addOption(inMemOption);
-		options.addOption(embedded);
-		options.addOption(clientserver);
-		options.addOption(dbProperties);
-		options.addOption(port);
-		options.addOption(startDB);
-		options.addOption(provenance);
-		options.addOption(logFileOption);
-
-		return options;
-
-	}
-
-	public boolean isClientServer() {
-		return hasOption("clientserver");
-	}
-
-	public boolean isEmbedded() {
-		return hasOption("embedded");
-	}
-
-	public boolean isInMemory() {
-		return hasOption("inmemory");
-	}
-
-	private CommandLine processArgs(String[] args) {
-		CommandLineParser parser = new GnuParser();
-		CommandLine line = null;
-		try {
-			// parse the command line arguments
-			line = parser.parse(options, args);
-		} catch (ParseException exp) {
-			// oops, something went wrong
-			System.err.println("Parsing failed.  Reason: " + exp.getMessage());
-			System.exit(1);
-		}
-		return line;
-	}
-
-	/**
-	 * Save the results to a directory if -output has been explicitly defined,
-	 * and/or if -outputdoc hasn't been defined
-	 * 
-	 * @return boolean
-	 */
-	public boolean saveResultsToDirectory() {
-		return (options.hasOption("outputdir") || !options
-				.hasOption("outputdoc"));
-	}
-}
diff --git a/taverna-commandline-1.2/taverna-commandline-common/src/main/resources/META-INF/services/net.sf.taverna.raven.launcher.Launchable b/taverna-commandline-1.2/taverna-commandline-common/src/main/resources/META-INF/services/net.sf.taverna.raven.launcher.Launchable
deleted file mode 100644
index 1314920..0000000
--- a/taverna-commandline-1.2/taverna-commandline-common/src/main/resources/META-INF/services/net.sf.taverna.raven.launcher.Launchable
+++ /dev/null
@@ -1 +0,0 @@
-net.sf.taverna.t2.commandline.CommandLineLauncher
\ No newline at end of file
diff --git a/taverna-commandline-1.2/taverna-commandline-common/src/main/resources/cl-log4j.properties b/taverna-commandline-1.2/taverna-commandline-common/src/main/resources/cl-log4j.properties
deleted file mode 100644
index 8c17461..0000000
--- a/taverna-commandline-1.2/taverna-commandline-common/src/main/resources/cl-log4j.properties
+++ /dev/null
@@ -1,27 +0,0 @@
-# By default, WARN (our external libraries)
-log4j.rootLogger=INFO, CONSOLE
-
-# Log INFO from anything Taverna
-log4j.logger.net.sf.taverna.t2=INFO
-
-
-
-# Restrict logging from classes that like to complain a lot
-log4j.logger.net.sf.taverna.raven=WARN
-log4j.logger.net.sf.taverna.t2.workbench.configuration.ConfigurationManager=WARN
-log4j.logger.net.sf.taverna.t2.workbench.views.graph.GraphViewComponent=WARN
-log4j.logger.net.sf.taverna.t2.workbench.ui.impl.WorkbenchPerspectives=WARN
-log4j.logger.net.sf.taverna.t2.workbench.ui.impl.DataflowEditsListener=WARN
-log4j.logger.net.sf.taverna.t2.workbench.ui.views.contextualviews.annotated.AnnotatedContextualView=WARN
-log4j.logger.net.sf.taverna.t2.workbench.ui.workflowview.WorkflowView=WARN
-log4j.logger.net.sf.taverna.t2.ui.menu.impl.MenuManagerImpl=ERROR
-
-log4j.logger.org.apache.commons.httpclient=ERROR
-
-
-# Default output to console is restrictive
-log4j.appender.CONSOLE=org.apache.log4j.ConsoleAppender
-log4j.appender.CONSOLE.layout=org.apache.log4j.PatternLayout
-log4j.appender.CONSOLE.layout.ConversionPattern=%-5p %d{ISO8601} (%c:%L) - %m%n
-# Output WARN and above to console - 
-log4j.appender.CONSOLE.Threshold=ERROR
\ No newline at end of file
diff --git a/taverna-commandline-1.2/taverna-commandline-common/src/main/resources/database-defaults.properties b/taverna-commandline-1.2/taverna-commandline-common/src/main/resources/database-defaults.properties
deleted file mode 100644
index 1080856..0000000
--- a/taverna-commandline-1.2/taverna-commandline-common/src/main/resources/database-defaults.properties
+++ /dev/null
@@ -1,11 +0,0 @@
-in_memory = true
-provenance = false
-connector = derby
-port = 1527 
-dialect = org.hibernate.dialect.DerbyDialect
-start_derby = false
-pool_max_active = 50
-pool_min_idle = 50
-pool_max_idle = 10
-driver = org.apache.derby.jdbc.EmbeddedDriver
-jdbcuri = jdbc:derby:t2-database;create=true;upgrade=true
\ No newline at end of file
diff --git a/taverna-commandline-1.2/taverna-commandline-common/src/main/resources/help.txt b/taverna-commandline-1.2/taverna-commandline-common/src/main/resources/help.txt
deleted file mode 100644
index 580ee42..0000000
--- a/taverna-commandline-1.2/taverna-commandline-common/src/main/resources/help.txt
+++ /dev/null
@@ -1,73 +0,0 @@
-By default, the workflow is executed using the -inmemory option, and the
-results are written out to a directory named after the workflow name.
-
-If this directory already exists then an new directory is created, and
-appended with _<n>, where n is incremented to the next available index.
-
-Results are written out to files named after the output port for that result.
-If a result is composed of lists, then a directory is created for the output
-port and individual list items are named after the list element index (with 1
-being the first index). The the output is the result of an error, the filename
-is appended with '.error'.
-
-You can provide your own output directory with the -outputdir option. There
-will be an error if the directory already exists.
-
-You can also record your results to a Baclava document using -outputdoc
-option.  The document will be overwritten if it already exists.
-
-Inputs can be provided in three ways. Both -inputfile and -inputvalue options
-can be used together; -inputdoc option must be used on its own. -inputfile and
--inputvalue options both take two additional arguments, the name of the port
-for the input, and either a file containing the input data, or the input value
-itself respectively.
-
-If one of more of you workflow inputs is described as a list, you can create a
-list by using the -inputdelimiter option, which may be used with either
--inputfile or -inputvalue. This option takes two parameters - an input name
-and the delimiter by which to split the input into a list.
-
-The delimiter may be a simple character, such as a comma or a new-line
-character, or a regular expression. The input string, or file, will then be
-converted into a list being split by the delimiter specified. Make sure to 
-put the delimiter character in quotes as it may be interpreted by the shell 
-as a special character, e.g. ;.
-
-If a list of greater depth (i.e. a list or lists or deeper) is required then
-you will need to use the -inputdoc option.  However, if you provide an input
-of lower depth to that required, then it will automatically be wrapped in one
-or more lists up to the required depth.  Providing an input of greater depth
-than that required will result in an error.
-
-If a workflow has a high memory requirement, then it may be better to run it
-using a database to store data rather than storing it in memory, which is the
-default option. There are three options for using a database:
-
--embedded option, runs with an embedded database. This is slightly faster than
-the -clientserver option (below), but has the limitation that only one
-executeworkflow script may be executed simultaneously.
-
--clientserver option allows the workflow to be executed backed by the database
-running as a server. By default a database is not started for you, but may be
-started using -startdb option.
-
--startdb option starts a database. It may be used without providing a workflow
-to allow a database to be started separately, allowing multiple simultaneous
-executeworkflow script runs.
-
-More advanced database configurations can be specified using -dbproperties
-option, allowing you to take full control over the database used. This takes a
-second argument, the filename of the propeties file, for which the following
-example contains the default settings used:
-
-in_memory = true
-provenance = false
-connector = derby
-port = 1527
-dialect = org.hibernate.dialect.DerbyDialect
-start_derby = false
-driver = org.apache.derby.jdbc.EmbeddedDriver
-jdbcuri = jdbc:derby:t2-database;create=true;upgrade=true
-
-Note that when using -dbproperties together with other options, the other
-options take precedence.
diff --git a/taverna-commandline-1.2/taverna-commandline-common/src/test/java/net/sf/taverna/t2/commandline/TestCommandLineOptionsHandler.java b/taverna-commandline-1.2/taverna-commandline-common/src/test/java/net/sf/taverna/t2/commandline/TestCommandLineOptionsHandler.java
deleted file mode 100644
index dddeba6..0000000
--- a/taverna-commandline-1.2/taverna-commandline-common/src/test/java/net/sf/taverna/t2/commandline/TestCommandLineOptionsHandler.java
+++ /dev/null
@@ -1,266 +0,0 @@
-package net.sf.taverna.t2.commandline;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertTrue;
-import net.sf.taverna.t2.commandline.exceptions.InvalidOptionException;
-import net.sf.taverna.t2.commandline.options.CommandLineOptions;
-
-import org.junit.Test;
-
-public class TestCommandLineOptionsHandler {
-
-	@Test
-	public void testWorkflowName() throws Exception {
-		CommandLineOptions handler = new CommandLineOptions(
-				new String[] { "myworkflow.t2flow" });
-		assertEquals("myworkflow.t2flow", handler.getWorkflow());
-	}	
-	
-	@Test
-	public void shouldShowHelp() throws Exception {
-		CommandLineOptions options = new CommandLineOptions(
-				new String[] { "-help" });
-		assertTrue(options.askedForHelp());
-		options = new CommandLineOptions(
-				new String[] {});
-		assertTrue(options.askedForHelp());
-		options = new CommandLineOptions(new String[] { "myworkflow.t2flow" });
-		assertFalse(options.askedForHelp());
-	}
-
-	@Test
-	public void getWorkflow() throws Exception {
-		CommandLineOptions options = new CommandLineOptions(
-				new String[] { "-help" });
-		assertNull(options.getWorkflow());
-		options = new CommandLineOptions(new String[] { "myworkflow.t2flow" });
-		assertEquals("myworkflow.t2flow", options.getWorkflow());
-	}
-
-	@Test(expected = InvalidOptionException.class)
-	public void cannotProvideInputFileAndInputDoc() throws Exception {
-		new CommandLineOptions(new String[] { "-inputfile", "fred", "fred.txt",
-				"-inputdoc", "myworkflow.t2flow" });
-	}
-	
-	@Test(expected = InvalidOptionException.class)
-	public void cannotProvideInputValueAndInputDoc() throws Exception {
-		new CommandLineOptions(new String[] { "-inputvalue", "fred", "fred.txt",
-				"-inputdoc", "myworkflow.t2flow" });
-	}
-	
-	@Test
-	public void canProvideInputValueAndFileTogether() throws Exception {
-		//should not be an error
-		new CommandLineOptions(new String[] { "-inputvalue", "fred", "abc",
-				"-inputfile","fred2","fred2.txt","myworkflow.t2flow" });
-	}
-
-	@Test
-	public void getInputs() throws Exception {
-		CommandLineOptions options = new CommandLineOptions(new String[] {
-				"-inputfile", "fred", "fred.txt", "myworkflow.t2flow" });
-		assertEquals(2, options.getInputFiles().length);
-		assertEquals("fred", options.getInputFiles()[0]);
-		assertEquals("fred.txt", options.getInputFiles()[1]);
-
-		options = new CommandLineOptions(new String[] { "-inputfile", "fred",
-				"fred.txt", "-inputfile", "fred2", "fred2.txt",
-				"myworkflow.t2flow" });
-		assertEquals(4, options.getInputFiles().length);
-		assertEquals("fred", options.getInputFiles()[0]);
-		assertEquals("fred.txt", options.getInputFiles()[1]);
-		assertEquals("fred2", options.getInputFiles()[2]);
-		assertEquals("fred2.txt", options.getInputFiles()[3]);
-
-		options = new CommandLineOptions(new String[] { "myworkflow.t2flow" });
-		assertNotNull(options.getInputFiles());
-		assertEquals(0, options.getInputFiles().length);
-
-	}
-
-	@Test
-	public void hasInputValue() throws Exception {
-		CommandLineOptions options = new CommandLineOptions(new String[] {
-				"-inputvalue", "fred", "abc", "myworkflow.t2flow" });
-		assertTrue(options.hasInputValues());
-
-		options = new CommandLineOptions(new String[] { "myworkflow.t2flow" });
-		assertFalse(options.hasInputValues());
-	}
-	
-	@Test
-	public void getInputValues() throws Exception {
-		CommandLineOptions options = new CommandLineOptions(new String[] {
-				"-inputvalue", "fred", "abc", "myworkflow.t2flow" });
-		assertEquals(2, options.getInputValues().length);
-
-		options = new CommandLineOptions(new String[] { "myworkflow.t2flow" });
-		assertNotNull(options.getInputValues());
-		assertEquals(0,options.getInputValues().length);
-	}
-
-	@Test
-	public void hasInputs() throws Exception {
-		CommandLineOptions options = new CommandLineOptions(new String[] {
-				"-inputfile", "fred", "fred.txt", "myworkflow.t2flow" });
-		assertTrue(options.hasInputFiles());
-
-		options = new CommandLineOptions(new String[] { "myworkflow.t2flow" });
-		assertFalse(options.hasInputFiles());
-	}	
-
-	@Test
-	public void noWorkflowNameButStartDB() throws Exception {
-		// should not throw an error
-		CommandLineOptions options = new CommandLineOptions(
-				new String[] { "-startdb" });
-		assertTrue(options.getStartDatabase());
-		assertTrue(options.getStartDatabaseOnly());
-	}
-
-	@Test
-	public void workflowNameAndStartDB() throws Exception {
-		// should not throw an error
-		CommandLineOptions options = new CommandLineOptions(new String[] {
-				"-startdb", "myworkflow.t2flow" });
-		assertTrue(options.getStartDatabase());
-		assertFalse(options.getStartDatabaseOnly());
-	}
-
-	@Test(expected = InvalidOptionException.class)
-	public void provenanceButNoDatabase() throws Exception {
-		new CommandLineOptions(new String[] { "-provenance",
-				"myworkflow.t2flow" });
-	}
-
-	@Test(expected = InvalidOptionException.class)
-	public void provenanceButNoDatabase2() throws Exception {
-		new CommandLineOptions(new String[] { "-provenance", "-inmemory",
-				"myworkflow.t2flow" });
-	}
-
-	@Test
-	public void provenanceDatabase() throws Exception {
-		// should be no errors
-		new CommandLineOptions(new String[] { "-provenance", "-embedded",
-				"myworkflow.t2flow" });
-		new CommandLineOptions(new String[] { "-provenance", "-clientserver",
-				"myworkflow.t2flow" });
-		new CommandLineOptions(new String[] { "-provenance", "-dbproperties",
-				"dbproperties.properties", "myworkflow.t2flow" });
-	}
-	
-	@Test
-	public void testHasInputDelimiter() throws Exception {
-		CommandLineOptions options = new CommandLineOptions(new String[] {
-				"-inputvalue","in1","1,2,3","-inputdelimiter","in1",",","-inputdelimiter","in2",",","myworkflow.t2flow" });
-		assertTrue(options.hasDelimiterFor("in1"));
-		assertTrue(options.hasDelimiterFor("in2"));
-		assertFalse(options.hasDelimiterFor("in3"));
-	}
-	
-	@Test(expected = InvalidOptionException.class)
-	public void testInputDelimiterInvalidWithInputDoc() throws Exception {
-		new CommandLineOptions(new String[] {
-				"-inputdoc","doc.xml","-inputdelimiter","in1",",","myworkflow.t2flow" });
-	}
-	
-	
-	@Test
-	public void testInputDelimiter() throws Exception {
-		CommandLineOptions options = new CommandLineOptions(new String[] {
-				"-inputvalue","in1","1,2,3","-inputdelimiter","in1",",","-inputdelimiter","in2","!","myworkflow.t2flow" });
-		assertEquals(",",options.inputDelimiter("in1"));
-		assertEquals("!",options.inputDelimiter("in2"));
-		assertNull(options.inputDelimiter("in3"));
-	}
-
-	@Test
-	public void testInMemory() throws Exception {
-		CommandLineOptions handler = new CommandLineOptions(new String[] {
-				"-inmemory", "myworkflow.t2flow" });
-		assertTrue(handler.hasOption("inmemory"));
-	}
-
-	@Test
-	public void testEmbedded() throws Exception {
-		CommandLineOptions handler = new CommandLineOptions(new String[] {
-				"-embedded", "myworkflow.t2flow" });
-		assertTrue(handler.hasOption("embedded"));
-	}
-
-	@Test
-	public void testClientServer() throws Exception {
-		CommandLineOptions handler = new CommandLineOptions(new String[] {
-				"-clientserver", "myworkflow.t2flow" });
-		assertTrue(handler.hasOption("clientserver"));
-	}
-
-	@Test(expected = InvalidOptionException.class)
-	public void testInvalidEmbeddedAndClientServer() throws Exception {
-		new CommandLineOptions(new String[] { "-clientserver", "-embedded",
-				"myworkflow.t2flow" });
-	}
-
-	@Test(expected = InvalidOptionException.class)
-	public void testInvalidEmbeddedAndMemory() throws Exception {
-		new CommandLineOptions(new String[] { "-embedded", "-inmemory",
-				"myworkflow.t2flow" });
-	}
-
-	@Test(expected = InvalidOptionException.class)
-	public void testInvalidClientServerAndInMemory() throws Exception {
-		new CommandLineOptions(new String[] { "-clientserver", "-inmemory",
-				"myworkflow.t2flow" });
-	}
-
-	@Test
-	public void isInMemory() throws Exception {
-		CommandLineOptions options = new CommandLineOptions(new String[] {
-				"-inmemory", "myworkflow.t2flow" });
-
-		assertTrue(options.isInMemory());
-		assertFalse(options.isClientServer());
-		assertFalse(options.isEmbedded());
-	}
-
-	@Test
-	public void isClientServer() throws Exception {
-		CommandLineOptions options = new CommandLineOptions(new String[] {
-				"-clientserver", "myworkflow.t2flow" });
-
-		assertTrue(options.isClientServer());
-		assertFalse(options.isInMemory());
-		assertFalse(options.isEmbedded());
-	}
-	
-	@Test
-	public void hasLogFile() throws Exception {
-		CommandLineOptions options = new CommandLineOptions(new String[] {
-				"-logfile","/tmp/logging", "myworkflow.t2flow" });
-
-		assertTrue(options.hasLogFile());
-		assertEquals("/tmp/logging", options.getLogFile());
-	}
-	
-	@Test(expected = InvalidOptionException.class)
-	public void hasLogFileNotValidWithoutWorkflow() throws Exception{
-		CommandLineOptions options = new CommandLineOptions(new String[] {
-				"-logfile","/tmp/logging"});
-	}
-
-	@Test
-	public void isEmbedded() throws Exception {
-		CommandLineOptions options = new CommandLineOptions(new String[] {
-				"-embedded", "myworkflow.t2flow" });
-
-		assertTrue(options.isEmbedded());
-		assertFalse(options.isInMemory());
-		assertFalse(options.isClientServer());
-	}
-
-}
diff --git a/taverna-commandline-1.2/taverna-commandline-common/src/test/java/net/sf/taverna/t2/commandline/TestDatabaseConfigurationHandler.java b/taverna-commandline-1.2/taverna-commandline-common/src/test/java/net/sf/taverna/t2/commandline/TestDatabaseConfigurationHandler.java
deleted file mode 100644
index 555a1a6..0000000
--- a/taverna-commandline-1.2/taverna-commandline-common/src/test/java/net/sf/taverna/t2/commandline/TestDatabaseConfigurationHandler.java
+++ /dev/null
@@ -1,20 +0,0 @@
-package net.sf.taverna.t2.commandline;
-
-import static org.junit.Assert.assertEquals;
-import net.sf.taverna.t2.commandline.data.DatabaseConfigurationHandler;
-import net.sf.taverna.t2.commandline.options.CommandLineOptions;
-import net.sf.taverna.t2.workbench.reference.config.DataManagementConfiguration;
-
-import org.junit.Test;
-
-public class TestDatabaseConfigurationHandler {
-
-	@Test
-	public void testDefaults() throws Exception {
-		CommandLineOptions opts = new CommandLineOptions(new String[]{"myworkflow.t2flow"});
-		DatabaseConfigurationHandler handler = new DatabaseConfigurationHandler(opts);
-		handler.configureDatabase();
-		assertEquals("org.apache.derby.jdbc.EmbeddedDriver", DataManagementConfiguration.getInstance().getDriverClassName());
-		assertEquals(false, DataManagementConfiguration.getInstance().getStartInternalDerbyServer());
-	}
-}